Search
Question: DESeq2 PCA plotting
0
gravatar for sam.far.7
10 days ago by
sam.far.70
sam.far.70 wrote:

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

ADD COMMENTlink modified 9 days ago by Michael Love20k • written 10 days ago by sam.far.70
0
gravatar for Michael Love
9 days ago by
Michael Love20k
United States
Michael Love20k wrote:

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 COMMENTlink written 9 days ago by Michael Love20k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 240 users visited in the last hour