diff --git a/04-exploratory-qc.md b/04-exploratory-qc.md index f75df042..9f271338 100644 --- a/04-exploratory-qc.md +++ b/04-exploratory-qc.md @@ -372,7 +372,19 @@ Useful tools for interactive exploratory data analysis for RNA-seq are [Glimma]( ```r -app <- iSEE(se) +## Convert DESeqDataSet object to a SingleCellExperiment object, in order to +## be able to store the PCA representation +sce <- as(dds, "SingleCellExperiment") + +## Add PCA to the 'reducedDim' slot +stopifnot(rownames(pcaData) == colnames(sce)) +reducedDim(sce, "PCA") <- as.matrix(pcaData[, c("PC1", "PC2")]) + +## Add variance-stabilized data as a new assay +stopifnot(colnames(vsd) == colnames(sce)) +assay(sce, "vsd") <- assay(vsd) + +app <- iSEE(sce) shiny::runApp(app) ``` diff --git a/fig/04-exploratory-qc-rendered-pca-exercise-1.png b/fig/04-exploratory-qc-rendered-pca-exercise-1.png index cb214694..ce91a2ce 100644 Binary files a/fig/04-exploratory-qc-rendered-pca-exercise-1.png and b/fig/04-exploratory-qc-rendered-pca-exercise-1.png differ diff --git a/md5sum.txt b/md5sum.txt index 828c1476..606cbb26 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -6,7 +6,7 @@ "episodes/01-intro-to-rnaseq.Rmd" "7cc3f4922347f6d5d9ef80dd31e84fbb" "site/built/01-intro-to-rnaseq.md" "2023-09-13" "episodes/02-setup.Rmd" "44ede89e11c54f154bacc1f5d4ee01f2" "site/built/02-setup.md" "2023-09-13" "episodes/03-import-annotate.Rmd" "f07c9513607ea7cbcd8041bf9bfd5f0e" "site/built/03-import-annotate.md" "2023-09-17" -"episodes/04-exploratory-qc.Rmd" "f4b0f8f545ff869019c245b1638af48d" "site/built/04-exploratory-qc.md" "2023-09-17" +"episodes/04-exploratory-qc.Rmd" "59d9cac581d1c736628534f8cf37f1b5" "site/built/04-exploratory-qc.md" "2023-09-18" "episodes/05-differential-expression.Rmd" "29ab3939367a0b3521cfd764929e3aee" "site/built/05-differential-expression.md" "2023-09-17" "episodes/06-extra-design.Rmd" "e4859b8e76bc6d0c8d5c598e1d00b37b" "site/built/06-extra-design.md" "2023-09-13" "episodes/07-gene-set-analysis.Rmd" "e7b69b6f2af11dfab883303e9a50981d" "site/built/07-gene-set-analysis.md" "2023-09-17"