My question: can I use a dataset for further analysis showing the following type of PCA plot, computed after a DESeq2 using the following code :
#here "spikes" refer to ERCC spike-in dds <- estimateSizeFactors(dds, controlGenes=match(spikes, rownames(dds))) dds <- estimateDispersions(dds) dds <- nbinomWaldTest(dds) rld <- rlog(dds) plotPCA(rld, ntop = 500)
As you can see, one control sample is grouped with the treated on the bottom right (and the 2 remaining controls are not grouped). Should I play with the
Please don't hesitate to ask if something is missing, I am a still newbee !