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Auto-generated via {sandpaper} Source : f1daa18 Branch : main Author : Charlotte Soneson <[email protected]> Time : 2023-09-18 11:45:03 +0000 Message : Merge pull request #84 from carpentries-incubator/make-sce-for-isee Add some more things to the object before calling iSEE
carpentries-incubator · Sep 18, 2023 · 3ac6125 · 3ac6125
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diff --git 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
diff --git 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"