I am using DESeq2 on 63 RNASeq samples.
The design used to explain the counts is based on the mutational status of 2 genes: ~GroupGene1+GroupGene2
I performed 3 PCA on this dataset:
1) on all the genes with rowSums(counts(dds)) > 10, that are in my case 36276 genes.
The PCA are similar between rlog, vsd and log2 transformation of the data
2&3) on the 2000 and 500 most variable genes, selected with ntop parameter from PCAplot().
Here the PCA are very different between rlog and vsd. With rlog, 2 samples are very large outliers, so the 61 other samples look pretty similar. With vsd, these 2 samples are not outliers.
Do it exist cases where rlog is not working ?
And have some of you already encountered this problem?
Thank you in advance