DESeq2 PCA plotting
1
0
Entering edit mode
sam.far.7 • 0
@samfar7-18628
Last seen 5.3 years ago

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

deseq2 michael love • 989 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 2 hours ago
United States

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

ADD COMMENT

Login before adding your answer.

Traffic: 816 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6