Hi,

I am using DESeq2 to analysis rna-seq data. When I plot PCA for all samples in two groups I can see a nice separation within two groups(500 samples vs 50 samples), However, when I am plotting PCAs for matched/paired samples (two groups of 50 samples), I could do not see that the samples are separated into two groups any more?

Thanks, 

Sami

You may try removing the subject effect using limma::removeBatchEffect from the transformed data and then replotting. 

https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-still-batches-in-the-pca-plot