diff --git a/R/runPDTMTAnalysis.R b/R/runPDTMTAnalysis.R
index 8a42fdb..eb72c9a 100644
--- a/R/runPDTMTAnalysis.R
+++ b/R/runPDTMTAnalysis.R
@@ -205,20 +205,30 @@
 #'
 #' @examples
 #' if (interactive()) {
-#' #    sampleAnnot <- read.delim(
-#' #        system.file("extdata/mq_example/1356_sampleAnnot.txt",
-#' #                                          package = "einprot"))
-#' #    ## Basic analysis
-#' #    out <- runPDTMTAnalysis(
-#' #        outputDir = tempdir(),
-#' #        outputBaseName = "PD_TMT_basic",
-#' #        species = "mouse",
-#' #        iColPattern = "",
-#' #        sampleAnnot = sampleAnnot,
-#' #        stringIdCol = NULL
-#' #    )
-#' #    ## Output file
-#' #    out
+#'     ## Basic analysis
+#'     out <- runPDTMTAnalysis(
+#'         outputDir = tempdir(),
+#'         outputBaseName = "PD_TMT_basic",
+#'         species = "baker's yeast",
+#'         iColPattern = "^Abundance.F.+.Sample.",
+#'         pdOutputFolder = system.file("extdata", "pdtmt_example",
+#'                                      package = "einprot"),
+#'         pdResultName = "Fig2_m23139_RTS_QC_varMods",
+#'         inputLevel = "Proteins",
+#'         pdAnalysisFile = system.file("extdata", "pdtmt_example",
+#'                           "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
+#'                           package = "einprot"),
+#'         sampleAnnot = data.frame(
+#'             sample = c("HIS4KO_S05", "HIS4KO_S06", "HIS4KO_S07", "HIS4KO_S08",
+#'                        "MET6KO_S01", "MET6KO_S02", "MET6KO_S03", "MET6KO_S04",
+#'                        "URA2KO_S09", "URA2KO_S10", "URA2KO_S11", "URA2KO_S12",
+#'                        "WT_S13", "WT_S14", "WT_S15", "WT_S16"),
+#'             group = c(rep("HIS4KO", 4), rep("MET6KO", 4), rep("URA2KO", 4),
+#'                       rep("WT", 4))),
+#'         stringIdCol = NULL
+#'     )
+#'     ## Output file
+#'     out
 #' }
 #'
 #' @returns Invisibly, the path to the compiled html report.
diff --git a/R/seqLogoApp.R b/R/seqLogoApp.R
index 6921b9d..f469b94 100644
--- a/R/seqLogoApp.R
+++ b/R/seqLogoApp.R
@@ -17,6 +17,14 @@
 #'     files exported from the shiny app.
 #' @param ... Additional arguments passed to \code{utils::read.csv}.
 #'
+#' @examples
+#' tbl <- data.frame(id = c("seq1", "seq2", "seq3"),
+#'                   seqWindow = c("LITKDHE", "RQMKQPE", "LSNKVHG"))
+#' tfile <- tempfile(fileext = "_seq.csv")
+#' write.table(tbl, file = tfile, row.names = FALSE,
+#'             col.names = TRUE, quote = TRUE, sep = ",")
+#' seqLogoApp(tfile)
+#'
 #' @importFrom shiny fluidPage fluidPage sidebarLayout sidebarPanel
 #'     mainPanel downloadButton plotOutput renderPlot reactive downloadHandler
 #'     shinyApp textOutput renderText
diff --git a/R/subtractBaseline.R b/R/subtractBaseline.R
index 4181272..3baf46f 100644
--- a/R/subtractBaseline.R
+++ b/R/subtractBaseline.R
@@ -20,6 +20,20 @@
 #'
 #' @returns Matrix with baseline-subtracted abundances.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#'
+#' ## Introduce artificial batch column
+#' sce$batch <- rep(c("B1", "B2", "B3"), 3)
+#' SummarizedExperiment::colData(sce)
+#' mat <- getMatSubtractedBaseline(sce, assayName = "log2_LFQ.intensity",
+#'                                 baselineGroup = "RBC_ctrl",
+#'                                 sceFull = sce)
+#' ## After the subtraction, the baseline samples are equalized across the
+#' ## different batches
+#' head(mat)
+#'
 #' @importFrom SummarizedExperiment assay assayNames
 #'
 getMatSubtractedBaseline <- function(sce, assayName, baselineGroup, sceFull) {
diff --git a/man/getMatSubtractedBaseline.Rd b/man/getMatSubtractedBaseline.Rd
index cf37b64..7d877e0 100644
--- a/man/getMatSubtractedBaseline.Rd
+++ b/man/getMatSubtractedBaseline.Rd
@@ -28,6 +28,21 @@ subtract the average value across a set of reference/background/baseline
 samples, and add the average across all the baseline samples to retain
 information about overall abundance. Typically used to adjust for varying
 baselines between batches, when a reference sample is included in each batch.
+}
+\examples{
+sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+                           package = "einprot"))
+
+## Introduce artificial batch column
+sce$batch <- rep(c("B1", "B2", "B3"), 3)
+SummarizedExperiment::colData(sce)
+mat <- getMatSubtractedBaseline(sce, assayName = "log2_LFQ.intensity",
+                                baselineGroup = "RBC_ctrl",
+                                sceFull = sce)
+## After the subtraction, the baseline samples are equalized across the
+## different batches
+head(mat)
+
 }
 \author{
 Charlotte Soneson
diff --git a/man/runPDTMTAnalysis.Rd b/man/runPDTMTAnalysis.Rd
index 3b2b027..7928e0d 100644
--- a/man/runPDTMTAnalysis.Rd
+++ b/man/runPDTMTAnalysis.Rd
@@ -342,20 +342,30 @@ Launch a workflow on quantifications obtained with
 }
 \examples{
 if (interactive()) {
-#    sampleAnnot <- read.delim(
-#        system.file("extdata/mq_example/1356_sampleAnnot.txt",
-#                                          package = "einprot"))
-#    ## Basic analysis
-#    out <- runPDTMTAnalysis(
-#        outputDir = tempdir(),
-#        outputBaseName = "PD_TMT_basic",
-#        species = "mouse",
-#        iColPattern = "",
-#        sampleAnnot = sampleAnnot,
-#        stringIdCol = NULL
-#    )
-#    ## Output file
-#    out
+    ## Basic analysis
+    out <- runPDTMTAnalysis(
+        outputDir = tempdir(),
+        outputBaseName = "PD_TMT_basic",
+        species = "baker's yeast",
+        iColPattern = "^Abundance.F.+.Sample.",
+        pdOutputFolder = system.file("extdata", "pdtmt_example",
+                                     package = "einprot"),
+        pdResultName = "Fig2_m23139_RTS_QC_varMods",
+        inputLevel = "Proteins",
+        pdAnalysisFile = system.file("extdata", "pdtmt_example",
+                          "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
+                          package = "einprot"),
+        sampleAnnot = data.frame(
+            sample = c("HIS4KO_S05", "HIS4KO_S06", "HIS4KO_S07", "HIS4KO_S08",
+                       "MET6KO_S01", "MET6KO_S02", "MET6KO_S03", "MET6KO_S04",
+                       "URA2KO_S09", "URA2KO_S10", "URA2KO_S11", "URA2KO_S12",
+                       "WT_S13", "WT_S14", "WT_S15", "WT_S16"),
+            group = c(rep("HIS4KO", 4), rep("MET6KO", 4), rep("URA2KO", 4),
+                      rep("WT", 4))),
+        stringIdCol = NULL
+    )
+    ## Output file
+    out
 }
 
 }
diff --git a/man/seqLogoApp.Rd b/man/seqLogoApp.Rd
index bf55c65..5664311 100644
--- a/man/seqLogoApp.Rd
+++ b/man/seqLogoApp.Rd
@@ -28,6 +28,15 @@ A shiny app object.
 Launch a shiny app that displays the provided csv file as an interactive
 table, and generates a sequence logo for the sequences in the
 \code{seqWindow} column.
+}
+\examples{
+tbl <- data.frame(id = c("seq1", "seq2", "seq3"),
+                  seqWindow = c("LITKDHE", "RQMKQPE", "LSNKVHG"))
+tfile <- tempfile(fileext = "_seq.csv")
+write.table(tbl, file = tfile, row.names = FALSE,
+            col.names = TRUE, quote = TRUE, sep = ",")
+seqLogoApp(tfile)
+
 }
 \author{
 Charlotte Soneson