diff --git a/DESCRIPTION b/DESCRIPTION
index d16cf302..fb334305 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 1.9.7
-Date: 2026-04-14
+Version: 1.9.8
+Date: 2026-04-18
 Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
                    comment = c(ORCID = "0000-0002-9908-3007")),
              person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="gladki.arkadiusz@gmail.com",
@@ -38,7 +38,7 @@ Imports:
     stats,
     stringr,
     SummarizedExperiment,
-    qs,
+    qs2,
     utils
 Suggests:
     BiocManager,
diff --git a/Dockerfile b/Dockerfile
index 77041aa5..ed35bc13 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,7 +10,7 @@ ARG GITHUB_TOKEN
 RUN mkdir -p /mnt/vol
 COPY rplatform/dependencies.yaml rplatform/.github_access_token.txt* /mnt/vol
 RUN echo "$GITHUB_TOKEN" >> /mnt/vol/.github_access_token.txt
-RUN Rscript -e 'BiocManager::install(c("BiocStyle", "qs"))'
+RUN Rscript -e 'BiocManager::install(c("BiocStyle", "qs2"))'
 RUN Rscript -e "gDRstyle::installAllDeps()"
 
 #================= Check & build package
diff --git a/NEWS.md b/NEWS.md
index a579b6cc..fc625dbe 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+## gDRutils 1.9.8 - 2026-04-18
+* migrate from `qs` to `qs2` package (`qs::qread` → `qs2::qs_read`, `qs::qsave` → `qs2::qs_save`)
+* update batch file extension from `.qs` to `.qs2`
+
 ## gDRutils 1.9.7 - 2026-04-14
 * add support for metadata in `merge_MAE`
 
diff --git a/R/combo.R b/R/combo.R
index 845a5537..74183aac 100644
--- a/R/combo.R
+++ b/R/combo.R
@@ -11,7 +11,7 @@
 #' @return list of data.table(s) with combo data
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs")
+#' mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs2")
 #' convert_combo_data_to_dt(mae[[1]])
 #'
 #' @export
diff --git a/R/concatentate_SEs.R b/R/concatentate_SEs.R
index 3468dcf6..0f115a5f 100644
--- a/R/concatentate_SEs.R
+++ b/R/concatentate_SEs.R
@@ -33,7 +33,7 @@ has_nested_field <- function(asy, nested_field) {
 #' @details Revert this operation using \code{promote_fields}.
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' se <- promote_fields(se, "ReadoutValue", 2)
 #' demote_fields(se, "ReadoutValue")
@@ -96,7 +96,7 @@ demote_fields <- function(se, fields) {
 #' @seealso demote_fields
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' se <- promote_fields(se, "ReadoutValue", 2)
 #' 
@@ -218,7 +218,7 @@ promote_fields <- function(se, fields, MARGIN = c(1, 2)) {
 #' @return A \code{BumpyMatrix} object aggregated by \code{FUN}.
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' assay <- SummarizedExperiment::assay(se)
 #' aggregate_assay(assay, FUN = mean, by = c("Barcode"))
diff --git a/R/convert_mae_se_assay_to_dt.R b/R/convert_mae_se_assay_to_dt.R
index af80c085..a294ec7e 100644
--- a/R/convert_mae_se_assay_to_dt.R
+++ b/R/convert_mae_se_assay_to_dt.R
@@ -28,7 +28,7 @@
 #' @return data.table representation of the data in \code{assay_name}.
 #'
 #' @examples
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' convert_se_assay_to_dt(se, "Metrics")
 #'
@@ -230,7 +230,7 @@ convert_se_assay_to_dt <- function(se,
 #' @seealso flatten convert_se_assay_to_dt
 #'
 #' @examples
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' convert_mae_assay_to_dt(mae, "Metrics")
 #'
 #' @export
@@ -306,7 +306,7 @@ convert_mae_assay_to_dt <- function(mae,
 #' @return data.table representation of the data in \code{assay_name} with added information from \code{colData}.
 #'
 #' @examples
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' convert_se_assay_to_custom_dt(se, "Metrics")
 #' convert_se_assay_to_custom_dt(se, "Metrics", output_table = "Metrics_raw")
@@ -349,8 +349,8 @@ convert_se_assay_to_custom_dt <- function(se,
   }
   
   if (output_table %in% c("Metrics", "Metrics_raw")) {
-    # SE*.qs files contain 'c50' column instead of the 'ec50' in the metrics
-    # this is a temporary fix that should be removed once data (qs files) is reprocessed
+    # SE*.qs2 files contain 'c50' column instead of the 'ec50' in the metrics
+    # this is a temporary fix that should be removed once data (qs2 files) is reprocessed
     data.table::setnames(dt, "c50", "ec50", skip_absent = TRUE)
     
     groups <- c("normalization_type", "fit_source")
diff --git a/R/duplicates.R b/R/duplicates.R
index 45a89be4..d16a3771 100644
--- a/R/duplicates.R
+++ b/R/duplicates.R
@@ -31,7 +31,7 @@ has_dt_duplicated_rows <- function(dt, col_names = NULL) {
 #' 
 #' @param dt data.table with assay data
 #' @examples
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 #' get_assay_req_uniq_cols(smetrics_data)
 #' @return charvec with columns required to have unique data
@@ -80,7 +80,7 @@ get_assay_req_uniq_cols <- function(dt) {
 #' @return logical flag indicating if a dt contains duplicated rows or not
 #' @keywords duplicates
 #' @examples
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 #' has_assay_dt_duplicated_rows(smetrics_data)
 #' @export
@@ -142,7 +142,7 @@ get_duplicated_rows <- function(x,
 #' @param output string with the output format to be returned
 #' @return integer vector or data.table with duplicated rows
 #' @examples
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 #' get_assay_dt_duplicated_rows(smetrics_data, output = "data")
 #' get_assay_dt_duplicated_rows(smetrics_data)
@@ -169,7 +169,7 @@ get_assay_dt_duplicated_rows <- function(dt, output = "index") {
 #' @param msg_f function to be used to throw the message
 #' @param preview_max_numb number of rows to preview if duplicates found
 #' @examples
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 #' throw_msg_if_duplicates(smetrics_data, assay_name = "Metrics", msg_f = futile.logger::flog.info)
 #' @return NULL
diff --git a/R/experiment_validators.R b/R/experiment_validators.R
index 27603182..ba83be94 100644
--- a/R/experiment_validators.R
+++ b/R/experiment_validators.R
@@ -38,7 +38,7 @@ validate_dimnames <- function(obj, obj2, skip_empty = TRUE) {
 #' @export
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' validate_se_assay_name(se, "RawTreated")
 #'
@@ -71,7 +71,7 @@ validate_se_assay_name <- function(se, name) {
 #' @export
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' validate_SE(se)
 #'
@@ -142,7 +142,7 @@ validate_SE <- function(se,
 #' @export
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' validate_MAE(mae)
 #' 
 #' @author Bartosz Czech <bartosz.czech@@contractors.roche.com>
diff --git a/R/fit_curves.R b/R/fit_curves.R
index 87c7b51e..5624bb97 100644
--- a/R/fit_curves.R
+++ b/R/fit_curves.R
@@ -444,7 +444,7 @@ predict_efficacy_from_conc <- function(c, x_inf, x_0, ec50, h) {
 #' @return A single numeric value for the predicted 'smooth' response.
 #' 
 #' @examples
-#' mae <- gDRutils::get_synthetic_data("combo_matrix")
+#' mae <- get_synthetic_data("combo_matrix")
 #' se <- mae[[gDRutils::get_supported_experiments("combo")]]
 #' dt_metrics <- gDRutils::convert_se_assay_to_dt(se[1, 1], "Metrics")[normalization_type == "RV"]
 #' predict_smooth_from_combo(conc_1 = 1.2, conc_2 = 9.8, metrics_merged = dt_metrics)
diff --git a/R/helpers-tests.R b/R/helpers-tests.R
index 6f4a02c3..d091c2eb 100644
--- a/R/helpers-tests.R
+++ b/R/helpers-tests.R
@@ -11,7 +11,7 @@
 #' @export
 get_testdata <- function() {
   
-  mae <- get_synthetic_data("finalMAE_small")
+  mae <- get_synthetic_data("finalMAE_small.qs2")
   raw_data <- convert_mae_assay_to_dt(mae, "Metrics")
   drug_names <- unique(raw_data$DrugName)
   cell_line_names <- unique(raw_data$CellLineName)
@@ -51,7 +51,7 @@ get_testdata <- function() {
 #' @export
 get_testdata_combo <- function() {
   
-  mae <- get_synthetic_data("finalMAE_combo_matrix")
+  mae <- get_synthetic_data("finalMAE_combo_matrix.qs2")
   raw_data <- convert_mae_assay_to_dt(mae, "Metrics")
   drug_names <- unique(raw_data$DrugName)
   cell_line_names <- unique(raw_data$CellLineName)
@@ -91,7 +91,7 @@ get_testdata_combo <- function() {
 #' @export
 get_testdata_codilution <- function() {
   
-  mae <- get_synthetic_data("finalMAE_combo_codilution_small")
+  mae <- get_synthetic_data("finalMAE_combo_codilution_small.qs2")
   raw_data <- convert_mae_assay_to_dt(mae, "Metrics")
   drug_names <- unique(raw_data$DrugName)
   cell_line_names <- unique(raw_data$CellLineName)
diff --git a/R/json_convert.R b/R/json_convert.R
index 69826665..a4b4a11f 100644
--- a/R/json_convert.R
+++ b/R/json_convert.R
@@ -9,7 +9,7 @@
 #' @return String representation of a JSON document.
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' convert_mae_to_json(mae)
 #' convert_mae_to_json(mae, with_experiments = FALSE)
 #' 
diff --git a/R/json_validate.R b/R/json_validate.R
index fc7a065d..c61fb728 100644
--- a/R/json_validate.R
+++ b/R/json_validate.R
@@ -69,7 +69,7 @@ validate_json <- function(json, schema_path) {
 #' @return Boolean of whether or not mae is valid
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' validate_mae_with_schema(mae)
 #' 
 #' @export
diff --git a/R/merge_SE.R b/R/merge_SE.R
index 87ff2ef7..01b03093 100644
--- a/R/merge_SE.R
+++ b/R/merge_SE.R
@@ -13,8 +13,8 @@
 #' @keywords SE_operators
 #'
 #' @examples
-#' mae1 <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
-#' mae2 <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
+#' mae1 <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
+#' mae2 <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
 #' merge_MAE(list(mae1 = mae1, mae2 = mae2), title = "Test", description = "Test MAE")
 #'
 #' @return Merged MultiAssayExperiment object.
@@ -149,7 +149,7 @@ merge_MAE <- function(MAElist,
 #' @keywords SE_operators
 #'
 #' @examples
-#' se1 <- get_synthetic_data("finalMAE_small")[[1]]
+#' se1 <- get_synthetic_data("finalMAE_small.qs2")[[1]]
 #' merge_SE(list(se1 = se1, se2 = se1))
 #'
 #' @return merged SummarizedExperiment object
@@ -248,7 +248,7 @@ merge_SE <- function(SElist,
 #' @return BumpyMatrix or list with data.table + BumpyMatrix
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
+#' mae <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
 #' 
 #' listSE <- list(
 #'   combo1 = mae[[1]], 
@@ -303,7 +303,7 @@ merge_assay <- function(SElist,
 #' @return character vector of unique names of metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' SElist <- list(
 #'   se, 
@@ -329,7 +329,7 @@ identify_unique_se_metadata_fields <- function(SElist) {
 #' @return list of merged metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' listSE <- list(
 #'   se, 
diff --git a/R/se_metadata.R b/R/se_metadata.R
index 91302174..5a16d733 100644
--- a/R/se_metadata.R
+++ b/R/se_metadata.R
@@ -76,7 +76,7 @@ set_SE_experiment_raw_data <- function(se, value) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' get_SE_fit_parameters(se)
 #' 
@@ -90,7 +90,7 @@ get_SE_fit_parameters <- function(se) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' meta <- get_SE_processing_metadata(se)
 #' 
@@ -103,7 +103,7 @@ get_SE_processing_metadata <- function(se) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' get_SE_experiment_raw_data(se)
 #' 
@@ -116,7 +116,7 @@ get_SE_experiment_raw_data <- function(se) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' get_SE_experiment_metadata(se)
 #' 
@@ -142,7 +142,7 @@ get_SE_keys <- function(se, key_type = NULL) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' get_SE_identifiers(se)
 #' 
@@ -175,7 +175,7 @@ get_SE_identifiers <- function(se, id_type = NULL, simplify = TRUE) {
 #' @return named list with identifiers for each SE
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' get_MAE_identifiers(mae)
 #' 
 #' @keywords SE_operators
diff --git a/R/standardize_MAE.R b/R/standardize_MAE.R
index d1c25ad3..818dbf7d 100644
--- a/R/standardize_MAE.R
+++ b/R/standardize_MAE.R
@@ -8,7 +8,7 @@
 #' @return mae a MultiAssayExperiment with default gDR identifiers
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' S4Vectors::metadata(mae[[1]])$identifiers$drug <- "druug"
 #' standardize_mae(mae)
 #' 
@@ -32,7 +32,7 @@ standardize_mae <- function(mae, use_default = TRUE) {
 #' @return se a SummarizedExperiment with default gDR identifiers
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' S4Vectors::metadata(se)$identifiers$drug <- "druug"
 #' standardize_se(se)
@@ -142,7 +142,7 @@ standardize_se <- function(se, use_default = TRUE) {
 #' @return a renamed DFrame object
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' rename_DFrame(SummarizedExperiment::rowData(mae[[1]]), c("Gnumber" = "Gnumber1"))
 #' 
 #' @export
@@ -165,7 +165,7 @@ rename_DFrame <- function(df, mapping_vector) {
 #' @return a renamed BumpyMatrix object
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' assay <- SummarizedExperiment::assay(se)
 #' rename_bumpy(assay, c("Concentration" = "conc"))
@@ -231,7 +231,7 @@ get_optional_rowdata_fields <- function(se) {
 #' @return refined colData
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' refine_coldata(SummarizedExperiment::colData(mae[[1]]), mae[[1]])
 #' 
 #' @export
@@ -263,7 +263,7 @@ refine_coldata <- function(cd, se, default_v = "Undefined") {
 #' @return refined rowData
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' refine_rowdata(SummarizedExperiment::colData(mae[[1]]), mae[[1]])
 #' 
 #' @export
diff --git a/R/utils.R b/R/utils.R
index 39f3b1c6..1720705a 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -105,7 +105,7 @@ assert_choices <- function(x, choices, ...) {
 #' @return list or vector depends on unify param
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' MAEpply(mae, SummarizedExperiment::assayNames)
 #' 
 #' @keywords package_utils
@@ -207,7 +207,7 @@ loop <- function(x,
                              paste0(fun_name, "_",
                                     unique_id, "_",
                                     start_index, "_of_",
-                                    total_iterations, "_batch.qs"))
+                                    total_iterations, "_batch.qs2"))
       file.exists(file_path)
     }, logical(1))
     
@@ -237,9 +237,9 @@ loop <- function(x,
                              paste0(fun_name, "_",
                                     unique_id, "_",
                                     start_index, "_of_",
-                                    total_iterations, "_batch.qs"))
+                                    total_iterations, "_batch.qs2"))
       if (file.exists(file_path)) {
-        batch_results <- qs::qread(file_path)
+        batch_results <- qs2::qs_read(file_path)
         final_results <- c(final_results, batch_results)
       }
     }
@@ -249,7 +249,7 @@ loop <- function(x,
                              paste0(fun_name, "_",
                                     unique_id, "_",
                                     start_index, "_of_",
-                                    total_iterations, "_batch.qs"))
+                                    total_iterations, "_batch.qs2"))
       if (file.exists(file_path)) {
         file.remove(file_path)
       }
@@ -276,10 +276,10 @@ loop <- function(x,
 #' @param FUN A user-defined function to apply to each element of the batch.
 #' @param ... Optional arguments passed to `FUN`.
 #'
-#' @return This function does not return a value. It saves the processed batch results to disk as a `.qs` file.
+#' @return This function does not return a value. It saves the processed batch results to disk as a `.qs2` file.
 #'
 #' @details The function applies `FUN` to each element in `batch`, saves the results to a file named
-#' according to the format `<fun_name>_<unique_id>_<start_index>_of_<total_iterations>_batch.qs`, and clears
+#' according to the format `<fun_name>_<unique_id>_<start_index>_of_<total_iterations>_batch.qs2`, and clears
 #' memory using `gc()` after saving.
 #'
 #' @examples
@@ -310,8 +310,8 @@ process_batch <- function(batch,
                          paste0(fun_name, "_",
                                 unique_id, "_",
                                 start_index, "_of_",
-                                total_iterations, "_batch.qs"))
-  qs::qsave(results, file_path)
+                                total_iterations, "_batch.qs2"))
+  qs2::qs_save(results, file_path)
   invisible(gc()) # clear memory after saving the batch
 }
 
@@ -329,7 +329,7 @@ process_batch <- function(batch,
 #' @return The original \code{se} object with a new assay, \code{out_assay_name}.
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' FUN <- function(x) {
 #'   data.table::data.table(Concentration = x$Concentration, CorrectedReadout = x$CorrectedReadout)
@@ -398,7 +398,7 @@ apply_bumpy_function <- function(se,
 #' @return logical
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' is_mae_empty(mae)
 #' 
 #' @keywords package_utils
@@ -419,7 +419,7 @@ is_mae_empty <- function(mae) {
 #' @return logical
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' is_any_exp_empty(mae)
 #' 
 #' @keywords package_utils
@@ -440,7 +440,7 @@ is_any_exp_empty <- function(mae) {
 #' @return logical
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' is_exp_empty(se)
 #' 
@@ -472,7 +472,7 @@ is_exp_empty <- function(exp) {
 #' @return charvec with non-empty experiments
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' get_non_empty_assays(mae)
 #' 
 #' @keywords package_utils
@@ -492,7 +492,7 @@ get_non_empty_assays <- function(mae) {
 #' @author Arkadiusz Gladki <arkadiusz.gladki@@contractors.roche.com>
 #' 
 #' @examples
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' mcolData(mae)
 #'
 #' @return data.table with all-experiments colData
@@ -515,7 +515,7 @@ mcolData <- function(mae) {
 #' @return data.table with all-experiments rowData
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' mrowData(mae)
 #'
 #' @author Arkadiusz Gladki <arkadiusz.gladki@@contractors.roche.com>
@@ -527,13 +527,13 @@ mrowData <- function(mae) {
 
 #' Get synthetic data from gDRtestData package
 #'
-#' @param qs qs filename
+#' @param qs dataset name or qs2 filename (e.g. \code{"small"} or \code{"finalMAE_small.qs2"})
 #' 
 #' @keywords package_utils
 #' @export
 #' 
-#' @examples 
-#' get_synthetic_data("finalMAE_small.qs") 
+#' @examples
+#' get_synthetic_data("finalMAE_small.qs2")
 #'
 #' @return loaded data
 #' 
@@ -542,15 +542,13 @@ get_synthetic_data <- function(qs) {
   if (!grepl("finalMAE", qs)) {
     qs <- paste("finalMAE", qs, sep = "_")
   }
-  # check if extension exist and is supported -`qs`, if not add one or replace
-  if (!grepl(".qs$", qs)) {
-    if (grepl(".RDS$", qs)) {
-      qs <- gsub(".RDS", ".qs", qs)
-    } else {
-      qs <- paste0(qs, ".qs")
-    }
+  # normalize extension to .qs2 (handles .qs, .RDS, or no extension)
+  qs <- sub("\\.qs$", ".qs2", qs)
+  qs <- sub("\\.RDS$", ".qs2", qs)
+  if (!grepl("\\.qs2$", qs)) {
+    qs <- paste0(qs, ".qs2")
   }
-  qs::qread(system.file("testdata", qs, package = "gDRtestData"))
+  qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
 }
 
 
@@ -713,11 +711,11 @@ average_biological_replicates_dt <- function(
 #' @param se SummarizedExperiment
 #' 
 #' @examples
-#' se <- get_synthetic_data("combo_matrix")[[1]]
+#' se <- get_synthetic_data("finalMAE_combo_matrix.qs2")[[1]]
 #' is_combo_data(se)
-#' se <- get_synthetic_data("combo_matrix")[[2]]
+#' se <- get_synthetic_data("finalMAE_combo_matrix.qs2")[[2]]
 #' is_combo_data(se)
-#' se <- get_synthetic_data("small")[[1]]
+#' se <- get_synthetic_data("finalMAE_small.qs2")[[1]]
 #' is_combo_data(se)
 #'
 #' @return logical
@@ -1060,7 +1058,7 @@ remove_drug_batch <- function(drug_vec,
 #'        
 #' @examples
 #' # single-agent data
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[get_supported_experiments("sa")]], "Metrics")
 #' saveraged_data <- convert_se_assay_to_dt(sdata[[get_supported_experiments("sa")]], "Averaged")
 #' smetrics_data_capped <- cap_assay_infinities(saveraged_data,
@@ -1068,7 +1066,7 @@ remove_drug_batch <- function(drug_vec,
 #'                                              experiment_name = "single-agent")
 #' 
 #' # combination data
-#' cdata <- get_synthetic_data("finalMAE_combo_matrix_small")
+#' cdata <- get_synthetic_data("finalMAE_combo_matrix_small.qs2")
 #' scaveraged_data <- convert_se_assay_to_dt(cdata[[get_supported_experiments("combo")]], "Averaged")
 #' scmetrics_data <- convert_se_assay_to_dt(cdata[[get_supported_experiments("combo")]], "Metrics")
 #' scmetrics_data_capped <- cap_assay_infinities(scaveraged_data,
diff --git a/man/MAEpply.Rd b/man/MAEpply.Rd
index b79b8da3..b2253e5d 100644
--- a/man/MAEpply.Rd
+++ b/man/MAEpply.Rd
@@ -23,7 +23,7 @@ list or vector depends on unify param
 Lapply through all the experiments in MultiAssayExperiment object
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 MAEpply(mae, SummarizedExperiment::assayNames)
 
 }
diff --git a/man/SE_metadata.Rd b/man/SE_metadata.Rd
index 5f6f8bf4..a6877935 100644
--- a/man/SE_metadata.Rd
+++ b/man/SE_metadata.Rd
@@ -66,23 +66,23 @@ For \code{*et_SE_fit_parameters}, get/set metadata for fit parameters
 used to construct the Metrics assay in a SummarizedExperiment object.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 se <- mae[[1]]
 get_SE_fit_parameters(se)
 
-mae <- get_synthetic_data("finalMAE_small.qs") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 se <- mae[[1]]
 meta <- get_SE_processing_metadata(se)
 
-mae <- get_synthetic_data("finalMAE_small.qs") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 se <- mae[[1]]
 get_SE_experiment_raw_data(se)
 
-mae <- get_synthetic_data("finalMAE_small.qs") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 se <- mae[[1]]
 get_SE_experiment_metadata(se)
 
-mae <- get_synthetic_data("finalMAE_small.qs") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 se <- mae[[1]]
 get_SE_identifiers(se)
 
diff --git a/man/aggregate_assay.Rd b/man/aggregate_assay.Rd
index 74e701c5..0bd7c9a0 100644
--- a/man/aggregate_assay.Rd
+++ b/man/aggregate_assay.Rd
@@ -20,7 +20,7 @@ A \code{BumpyMatrix} object aggregated by \code{FUN}.
 Aggregation can only be performed on nested variables.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 se <- mae[[1]]
 assay <- SummarizedExperiment::assay(se)
 aggregate_assay(assay, FUN = mean, by = c("Barcode"))
diff --git a/man/apply_bumpy_function.Rd b/man/apply_bumpy_function.Rd
index a8c4fb73..7682aa9c 100644
--- a/man/apply_bumpy_function.Rd
+++ b/man/apply_bumpy_function.Rd
@@ -34,7 +34,7 @@ The original \code{se} object with a new assay, \code{out_assay_name}.
 Apply a user-specified function to every element of a bumpy matrix.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 FUN <- function(x) {
   data.table::data.table(Concentration = x$Concentration, CorrectedReadout = x$CorrectedReadout)
diff --git a/man/cap_assay_infinities.Rd b/man/cap_assay_infinities.Rd
index baca5abe..091ea974 100644
--- a/man/cap_assay_infinities.Rd
+++ b/man/cap_assay_infinities.Rd
@@ -40,7 +40,7 @@ Cap infinity values (Inf, -Inf) in the assay data
 }
 \examples{
 # single-agent data
-sdata <- get_synthetic_data("finalMAE_small")
+sdata <- get_synthetic_data("finalMAE_small.qs2")
 smetrics_data <- convert_se_assay_to_dt(sdata[[get_supported_experiments("sa")]], "Metrics")
 saveraged_data <- convert_se_assay_to_dt(sdata[[get_supported_experiments("sa")]], "Averaged")
 smetrics_data_capped <- cap_assay_infinities(saveraged_data,
@@ -48,7 +48,7 @@ smetrics_data_capped <- cap_assay_infinities(saveraged_data,
                                              experiment_name = "single-agent")
 
 # combination data
-cdata <- get_synthetic_data("finalMAE_combo_matrix_small")
+cdata <- get_synthetic_data("finalMAE_combo_matrix_small.qs2")
 scaveraged_data <- convert_se_assay_to_dt(cdata[[get_supported_experiments("combo")]], "Averaged")
 scmetrics_data <- convert_se_assay_to_dt(cdata[[get_supported_experiments("combo")]], "Metrics")
 scmetrics_data_capped <- cap_assay_infinities(scaveraged_data,
diff --git a/man/convert_combo_data_to_dt.Rd b/man/convert_combo_data_to_dt.Rd
index 480bf02c..f127dd24 100644
--- a/man/convert_combo_data_to_dt.Rd
+++ b/man/convert_combo_data_to_dt.Rd
@@ -27,7 +27,7 @@ list of data.table(s) with combo data
 convert combo assays from SummarizedExperiments to the list of data.tables
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs")
+mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs2")
 convert_combo_data_to_dt(mae[[1]])
 
 }
diff --git a/man/convert_mae_assay_to_dt.Rd b/man/convert_mae_assay_to_dt.Rd
index 9a3a8efc..9d9bbe67 100644
--- a/man/convert_mae_assay_to_dt.Rd
+++ b/man/convert_mae_assay_to_dt.Rd
@@ -55,7 +55,7 @@ NOTE: to extract information about 'Control' data, simply call the
 function with the name of the assay holding data on controls.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 convert_mae_assay_to_dt(mae, "Metrics")
 
 }
diff --git a/man/convert_mae_to_json.Rd b/man/convert_mae_to_json.Rd
index e146ba90..7a1a526c 100644
--- a/man/convert_mae_to_json.Rd
+++ b/man/convert_mae_to_json.Rd
@@ -18,7 +18,7 @@ String representation of a JSON document.
 Convert a MultiAssayExperiment object to a JSON document.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 convert_mae_to_json(mae)
 convert_mae_to_json(mae, with_experiments = FALSE)
 
diff --git a/man/convert_se_assay_to_custom_dt.Rd b/man/convert_se_assay_to_custom_dt.Rd
index 714b8aca..cabb10a9 100644
--- a/man/convert_se_assay_to_custom_dt.Rd
+++ b/man/convert_se_assay_to_custom_dt.Rd
@@ -56,7 +56,7 @@ function with the name of the assay holding data on controls.
 To extract the reference data in the same format as 'Averaged' use \code{convert_se_ref_assay_to_dt}.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 convert_se_assay_to_custom_dt(se, "Metrics")
 convert_se_assay_to_custom_dt(se, "Metrics", output_table = "Metrics_raw")
diff --git a/man/convert_se_assay_to_dt.Rd b/man/convert_se_assay_to_dt.Rd
index d19bc809..e1e61f0c 100644
--- a/man/convert_se_assay_to_dt.Rd
+++ b/man/convert_se_assay_to_dt.Rd
@@ -53,7 +53,7 @@ function with the name of the assay holding data on controls.
 To extract the reference data in to same format as 'Averaged' use \code{convert_se_ref_assay_to_dt}.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 convert_se_assay_to_dt(se, "Metrics")
 
diff --git a/man/demote_fields.Rd b/man/demote_fields.Rd
index 6ed2389d..cf24cc3f 100644
--- a/man/demote_fields.Rd
+++ b/man/demote_fields.Rd
@@ -24,7 +24,7 @@ to a nested field of a \code{BumpyMatrix} assay.
 Revert this operation using \code{promote_fields}.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 se <- promote_fields(se, "ReadoutValue", 2)
 demote_fields(se, "ReadoutValue")
diff --git a/man/get_MAE_identifiers.Rd b/man/get_MAE_identifiers.Rd
index a444d831..7110b2b9 100644
--- a/man/get_MAE_identifiers.Rd
+++ b/man/get_MAE_identifiers.Rd
@@ -16,7 +16,7 @@ named list with identifiers for each SE
 get the identifiers of all SE's in the MAE
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 get_MAE_identifiers(mae)
 
 }
diff --git a/man/get_assay_dt_duplicated_rows.Rd b/man/get_assay_dt_duplicated_rows.Rd
index 43111dc0..f985c7ef 100644
--- a/man/get_assay_dt_duplicated_rows.Rd
+++ b/man/get_assay_dt_duplicated_rows.Rd
@@ -18,7 +18,7 @@ integer vector or data.table with duplicated rows
 Helper function to find duplicated rows in assay data
 }
 \examples{
-sdata <- get_synthetic_data("finalMAE_small")
+sdata <- get_synthetic_data("finalMAE_small.qs2")
 smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 get_assay_dt_duplicated_rows(smetrics_data, output = "data")
 get_assay_dt_duplicated_rows(smetrics_data)
diff --git a/man/get_assay_req_uniq_cols.Rd b/man/get_assay_req_uniq_cols.Rd
index 91ea6ff0..22a3bc62 100644
--- a/man/get_assay_req_uniq_cols.Rd
+++ b/man/get_assay_req_uniq_cols.Rd
@@ -16,7 +16,7 @@ charvec with columns required to have unique data
 get columns in the assay data required to have unique (non-duplicated) data
 }
 \examples{
-sdata <- get_synthetic_data("finalMAE_small")
+sdata <- get_synthetic_data("finalMAE_small.qs2")
 smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 get_assay_req_uniq_cols(smetrics_data)
 }
diff --git a/man/get_non_empty_assays.Rd b/man/get_non_empty_assays.Rd
index c9685bf4..bca45d32 100644
--- a/man/get_non_empty_assays.Rd
+++ b/man/get_non_empty_assays.Rd
@@ -16,7 +16,7 @@ charvec with non-empty experiments
 get non empty assays
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 get_non_empty_assays(mae)
 
 }
diff --git a/man/get_synthetic_data.Rd b/man/get_synthetic_data.Rd
index 0289f98d..78f0cc39 100644
--- a/man/get_synthetic_data.Rd
+++ b/man/get_synthetic_data.Rd
@@ -7,7 +7,7 @@
 get_synthetic_data(qs)
 }
 \arguments{
-\item{qs}{qs filename}
+\item{qs}{dataset name or qs2 filename (e.g. \code{"small"} or \code{"finalMAE_small.qs2"})}
 }
 \value{
 loaded data
@@ -16,7 +16,7 @@ loaded data
 Get synthetic data from gDRtestData package
 }
 \examples{
-get_synthetic_data("finalMAE_small.qs") 
+get_synthetic_data("finalMAE_small.qs2")
 
 }
 \keyword{package_utils}
diff --git a/man/has_assay_dt_duplicated_rows.Rd b/man/has_assay_dt_duplicated_rows.Rd
index 0c67d6ab..1e6e2425 100644
--- a/man/has_assay_dt_duplicated_rows.Rd
+++ b/man/has_assay_dt_duplicated_rows.Rd
@@ -16,7 +16,7 @@ logical flag indicating if a dt contains duplicated rows or not
 An auxiliary function that checks for duplicates in the assay data
 }
 \examples{
-sdata <- get_synthetic_data("finalMAE_small")
+sdata <- get_synthetic_data("finalMAE_small.qs2")
 smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 has_assay_dt_duplicated_rows(smetrics_data)
 }
diff --git a/man/identify_unique_se_metadata_fields.Rd b/man/identify_unique_se_metadata_fields.Rd
index b2ea2a59..465ee700 100644
--- a/man/identify_unique_se_metadata_fields.Rd
+++ b/man/identify_unique_se_metadata_fields.Rd
@@ -16,7 +16,7 @@ character vector of unique names of metadata
 Identify unique metadata fields from a list of \code{SummarizedExperiment}s
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 SElist <- list(
   se, 
diff --git a/man/is_any_exp_empty.Rd b/man/is_any_exp_empty.Rd
index d6f10e1e..1e6da96c 100644
--- a/man/is_any_exp_empty.Rd
+++ b/man/is_any_exp_empty.Rd
@@ -16,7 +16,7 @@ logical
 check if any experiment is empty
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 is_any_exp_empty(mae)
 
 }
diff --git a/man/is_combo_data.Rd b/man/is_combo_data.Rd
index dab1df45..3644441f 100644
--- a/man/is_combo_data.Rd
+++ b/man/is_combo_data.Rd
@@ -16,11 +16,11 @@ logical
 Checks if \code{se} is combo dataset.
 }
 \examples{
-se <- get_synthetic_data("combo_matrix")[[1]]
+se <- get_synthetic_data("finalMAE_combo_matrix.qs2")[[1]]
 is_combo_data(se)
-se <- get_synthetic_data("combo_matrix")[[2]]
+se <- get_synthetic_data("finalMAE_combo_matrix.qs2")[[2]]
 is_combo_data(se)
-se <- get_synthetic_data("small")[[1]]
+se <- get_synthetic_data("finalMAE_small.qs2")[[1]]
 is_combo_data(se)
 
 }
diff --git a/man/is_exp_empty.Rd b/man/is_exp_empty.Rd
index 100006c7..fb331179 100644
--- a/man/is_exp_empty.Rd
+++ b/man/is_exp_empty.Rd
@@ -16,7 +16,7 @@ logical
 check if experiment (SE) is empty
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 is_exp_empty(se)
 
diff --git a/man/is_mae_empty.Rd b/man/is_mae_empty.Rd
index ce7b9d79..12d4987f 100644
--- a/man/is_mae_empty.Rd
+++ b/man/is_mae_empty.Rd
@@ -16,7 +16,7 @@ logical
 check if all mae experiments are empty
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 is_mae_empty(mae)
 
 }
diff --git a/man/mcolData.Rd b/man/mcolData.Rd
index f8869684..ebd84d60 100644
--- a/man/mcolData.Rd
+++ b/man/mcolData.Rd
@@ -16,7 +16,7 @@ data.table with all-experiments colData
 get colData of all experiments
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 mcolData(mae)
 
 }
diff --git a/man/merge_MAE.Rd b/man/merge_MAE.Rd
index b0744b20..bc34a995 100644
--- a/man/merge_MAE.Rd
+++ b/man/merge_MAE.Rd
@@ -40,8 +40,8 @@ Merged MultiAssayExperiment object.
 Merge multiple MultiAssayExperiment objects
 }
 \examples{
-mae1 <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
-mae2 <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
+mae1 <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
+mae2 <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
 merge_MAE(list(mae1 = mae1, mae2 = mae2), title = "Test", description = "Test MAE")
 
 }
diff --git a/man/merge_SE.Rd b/man/merge_SE.Rd
index bd203036..e7067524 100644
--- a/man/merge_SE.Rd
+++ b/man/merge_SE.Rd
@@ -28,7 +28,7 @@ merged SummarizedExperiment object
 Merge multiple Summarized Experiments
 }
 \examples{
-se1 <- get_synthetic_data("finalMAE_small")[[1]]
+se1 <- get_synthetic_data("finalMAE_small.qs2")[[1]]
 merge_SE(list(se1 = se1, se2 = se1))
 
 }
diff --git a/man/merge_assay.Rd b/man/merge_assay.Rd
index 5a68f1b5..c296dbe7 100644
--- a/man/merge_assay.Rd
+++ b/man/merge_assay.Rd
@@ -30,7 +30,7 @@ BumpyMatrix or list with data.table + BumpyMatrix
 Merge assay data
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
+mae <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
 
 listSE <- list(
   combo1 = mae[[1]], 
diff --git a/man/merge_metadata.Rd b/man/merge_metadata.Rd
index 6ef777c7..38782eb9 100644
--- a/man/merge_metadata.Rd
+++ b/man/merge_metadata.Rd
@@ -18,7 +18,7 @@ list of merged metadata
 Merge metadata
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 listSE <- list(
   se, 
diff --git a/man/mrowData.Rd b/man/mrowData.Rd
index ad27f758..1a90bae1 100644
--- a/man/mrowData.Rd
+++ b/man/mrowData.Rd
@@ -16,7 +16,7 @@ data.table with all-experiments rowData
 get rowData of all experiments
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 mrowData(mae)
 
 }
diff --git a/man/predict_smooth_from_combo.Rd b/man/predict_smooth_from_combo.Rd
index 4f04f407..dfba6236 100644
--- a/man/predict_smooth_from_combo.Rd
+++ b/man/predict_smooth_from_combo.Rd
@@ -24,7 +24,7 @@ their predictions. This is the combination equivalent of
 'predict_efficacy_from_conc'.
 }
 \examples{
-mae <- gDRutils::get_synthetic_data("combo_matrix")
+mae <- get_synthetic_data("combo_matrix")
 se <- mae[[gDRutils::get_supported_experiments("combo")]]
 dt_metrics <- gDRutils::convert_se_assay_to_dt(se[1, 1], "Metrics")[normalization_type == "RV"]
 predict_smooth_from_combo(conc_1 = 1.2, conc_2 = 9.8, metrics_merged = dt_metrics)
diff --git a/man/process_batch.Rd b/man/process_batch.Rd
index e2a4c60c..87541e83 100644
--- a/man/process_batch.Rd
+++ b/man/process_batch.Rd
@@ -33,14 +33,14 @@ process_batch(
 \item{...}{Optional arguments passed to \code{FUN}.}
 }
 \value{
-This function does not return a value. It saves the processed batch results to disk as a \code{.qs} file.
+This function does not return a value. It saves the processed batch results to disk as a \code{.qs2} file.
 }
 \description{
 Process and save a batch of results.
 }
 \details{
 The function applies \code{FUN} to each element in \code{batch}, saves the results to a file named
-according to the format \verb{<fun_name>_<unique_id>_<start_index>_of_<total_iterations>_batch.qs}, and clears
+according to the format \verb{<fun_name>_<unique_id>_<start_index>_of_<total_iterations>_batch.qs2}, and clears
 memory using \code{gc()} after saving.
 }
 \examples{
diff --git a/man/promote_fields.Rd b/man/promote_fields.Rd
index 8d504758..6ef9c745 100644
--- a/man/promote_fields.Rd
+++ b/man/promote_fields.Rd
@@ -27,7 +27,7 @@ as either the \code{rowData} or \code{colData}.
 Revert this operation using \code{demote_fields}.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 se <- promote_fields(se, "ReadoutValue", 2)
 
diff --git a/man/refine_coldata.Rd b/man/refine_coldata.Rd
index 97b61fb9..799b6d4a 100644
--- a/man/refine_coldata.Rd
+++ b/man/refine_coldata.Rd
@@ -23,7 +23,7 @@ current improvements done on the colData as a standardization step:
 }
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 refine_coldata(SummarizedExperiment::colData(mae[[1]]), mae[[1]])
 
 }
diff --git a/man/refine_rowdata.Rd b/man/refine_rowdata.Rd
index ee47eb51..b1b2a91e 100644
--- a/man/refine_rowdata.Rd
+++ b/man/refine_rowdata.Rd
@@ -23,7 +23,7 @@ current improvements done on the rowData as a standardization step:
 }
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 refine_rowdata(SummarizedExperiment::colData(mae[[1]]), mae[[1]])
 
 }
diff --git a/man/rename_DFrame.Rd b/man/rename_DFrame.Rd
index 64a39b99..84d401c2 100644
--- a/man/rename_DFrame.Rd
+++ b/man/rename_DFrame.Rd
@@ -20,7 +20,7 @@ a renamed DFrame object
 Rename DFrame
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 rename_DFrame(SummarizedExperiment::rowData(mae[[1]]), c("Gnumber" = "Gnumber1"))
 
 }
diff --git a/man/rename_bumpy.Rd b/man/rename_bumpy.Rd
index 0047316c..f49fb9b7 100644
--- a/man/rename_bumpy.Rd
+++ b/man/rename_bumpy.Rd
@@ -20,7 +20,7 @@ a renamed BumpyMatrix object
 Rename BumpyMatrix
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 assay <- SummarizedExperiment::assay(se)
 rename_bumpy(assay, c("Concentration" = "conc"))
diff --git a/man/split_big_table_for_xlsx.Rd b/man/split_big_table_for_xlsx.Rd
index 72cb79c6..a52b9b80 100644
--- a/man/split_big_table_for_xlsx.Rd
+++ b/man/split_big_table_for_xlsx.Rd
@@ -4,7 +4,7 @@
 \alias{split_big_table_for_xlsx}
 \title{Split big table}
 \usage{
-split_big_table_for_xlsx(dt_list, max_row = 1000000, max_col = 16000)
+split_big_table_for_xlsx(dt_list, max_row = 1e+06, max_col = 16000)
 }
 \arguments{
 \item{dt_list}{list of data.tables. Each data.table will be checked and
diff --git a/man/standardize_mae.Rd b/man/standardize_mae.Rd
index 8f4c5780..e98a1c91 100644
--- a/man/standardize_mae.Rd
+++ b/man/standardize_mae.Rd
@@ -19,7 +19,7 @@ mae a MultiAssayExperiment with default gDR identifiers
 Standardize MAE by switching from custom identifiers into gDR-default
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 S4Vectors::metadata(mae[[1]])$identifiers$drug <- "druug"
 standardize_mae(mae)
 
diff --git a/man/standardize_se.Rd b/man/standardize_se.Rd
index 30084f08..ef9f558e 100644
--- a/man/standardize_se.Rd
+++ b/man/standardize_se.Rd
@@ -19,7 +19,7 @@ se a SummarizedExperiment with default gDR identifiers
 Standardize SE by switching from custom identifiers into gDR-default
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small.qs")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 S4Vectors::metadata(se)$identifiers$drug <- "druug"
 standardize_se(se)
diff --git a/man/throw_msg_if_duplicates.Rd b/man/throw_msg_if_duplicates.Rd
index ad80b3c5..0824efb9 100644
--- a/man/throw_msg_if_duplicates.Rd
+++ b/man/throw_msg_if_duplicates.Rd
@@ -26,7 +26,7 @@ In case of duplicates it throws a message. The messsage function is by default \
 The message function can be customized with \code{msg_f} parameter
 }
 \examples{
-sdata <- get_synthetic_data("finalMAE_small")
+sdata <- get_synthetic_data("finalMAE_small.qs2")
 smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 throw_msg_if_duplicates(smetrics_data, assay_name = "Metrics", msg_f = futile.logger::flog.info)
 }
diff --git a/man/validate_MAE.Rd b/man/validate_MAE.Rd
index f75701a9..0bcd1df5 100644
--- a/man/validate_MAE.Rd
+++ b/man/validate_MAE.Rd
@@ -25,7 +25,7 @@ Function validates correctness of SE included in MAE by checking multiple cases:
 }
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 validate_MAE(mae)
 
 }
diff --git a/man/validate_SE.Rd b/man/validate_SE.Rd
index 542b7cc2..f55a5be4 100644
--- a/man/validate_SE.Rd
+++ b/man/validate_SE.Rd
@@ -28,7 +28,7 @@ Function validates correctness of SE by checking multiple cases:
 }
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small")
+mae <- get_synthetic_data("finalMAE_small.qs2")
 se <- mae[[1]]
 validate_SE(se)
 
diff --git a/man/validate_mae_with_schema.Rd b/man/validate_mae_with_schema.Rd
index b71ea9f9..7e90cd22 100644
--- a/man/validate_mae_with_schema.Rd
+++ b/man/validate_mae_with_schema.Rd
@@ -29,7 +29,7 @@ Currently only SEs are validated
 TODO: add mae.json schema and validate full MAE object
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 validate_mae_with_schema(mae)
 
 }
diff --git a/man/validate_se_assay_name.Rd b/man/validate_se_assay_name.Rd
index d9ccb1be..b5fd96fc 100644
--- a/man/validate_se_assay_name.Rd
+++ b/man/validate_se_assay_name.Rd
@@ -19,7 +19,7 @@ Throws an error if the assay is not valid.
 Check for the presence of an assay in a SummarizedExperiment object.
 }
 \examples{
-mae <- get_synthetic_data("finalMAE_small") 
+mae <- get_synthetic_data("finalMAE_small.qs2") 
 se <- mae[[1]]
 validate_se_assay_name(se, "RawTreated")
 
diff --git a/tests/testthat/test-merge_SE.R b/tests/testthat/test-merge_SE.R
index c7d7928b..25671de2 100644
--- a/tests/testthat/test-merge_SE.R
+++ b/tests/testthat/test-merge_SE.R
@@ -1,19 +1,19 @@
 listMAE <- lapply(list.files(system.file(package = "gDRtestData", "testdata"),
-                             "final", full.names = TRUE)[1:2], qs::qread)
+                             "final.*\\.qs2$", full.names = TRUE)[1:2], qs2::qs_read)
 names(listMAE) <- c("MAE1", "MAE2")
 listSE <- lapply(listMAE, function(x) x[[2]])
 names(listSE) <- c("combo1", "combo2")
 
 listMAE2 <- lapply(list.files(system.file(package = "gDRtestData", "testdata"),
-                              "final", full.names = TRUE)[1:2], qs::qread)
+                             "final.*\\.qs2$", full.names = TRUE)[1:2], qs2::qs_read)
 listSE2 <- lapply(listMAE, function(x) x[[1]])
 names(listSE2) <- c("combo1", "combo2")
 
 listSE3 <- c(listSE[1], listSE2[2])
 
-listSE4 <- c(listSE[1], ligand = qs::qread(
+listSE4 <- c(listSE[1], ligand = qs2::qs_read(
   list.files(system.file(package = "gDRtestData", "testdata"),
-             "Ligand", full.names = TRUE))[[1]])
+             "Ligand.*\\.qs2$", full.names = TRUE)[1])[[1]])
 
 
 test_that("merge_assay works as expected", {
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 04fa5aa2..691d39c4 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -187,10 +187,10 @@ test_that("process_batch works as expected", {
   process_batch(namedBatch, start_index = 1, fun_name = "test_fun", unique_id = "test_id", 
                 total_iterations = n, temp_dir = temp_dir, FUN = sum)
   
-  file_path <- file.path(temp_dir, "test_fun_test_id_1_of_50_batch.qs")
+  file_path <- file.path(temp_dir, "test_fun_test_id_1_of_50_batch.qs2")
   expect_true(file.exists(file_path))
-  
-  saved_results <- qs::qread(file_path)
+
+  saved_results <- qs2::qs_read(file_path)
   expect_true(is.list(saved_results))
   expect_length(saved_results, n)
   expect_equal(names(saved_results), names(namedBatch))
@@ -200,12 +200,12 @@ test_that("process_batch works as expected", {
   process_batch(list(), start_index = 1, fun_name = "test_fun", unique_id = "test_id", 
                 total_iterations = 1, temp_dir = temp_dir, FUN = sum)
   
-  empty_file_path <- file.path(temp_dir, "test_fun_test_id_1_of_0_batch.qs")
+  empty_file_path <- file.path(temp_dir, "test_fun_test_id_1_of_0_batch.qs2")
   expect_false(file.exists(empty_file_path))
 })
 
 test_that("get_synthetic_data works as expected", {
-  expect_is(get_synthetic_data("finalMAE_small.qs"),
+  expect_is(get_synthetic_data("finalMAE_small.qs2"),
             "MultiAssayExperiment")
   expect_is(get_synthetic_data("finalMAE_small"),
             "MultiAssayExperiment")