diff --git a/episodes/04-exploratory-qc.Rmd b/episodes/04-exploratory-qc.Rmd index ef918abe..cf788c93 100644 --- a/episodes/04-exploratory-qc.Rmd +++ b/episodes/04-exploratory-qc.Rmd @@ -319,7 +319,19 @@ Useful tools for interactive exploratory data analysis for RNA-seq are [Glimma]( ## Challenge: Interactively explore our data using iSEE ```{r isee, eval=FALSE} -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) ```