Should I normalize read counts if I want to run plotPCA?
1
0
Entering edit mode
cupret • 0
@cupret-21426
Last seen 17 months ago

Hi, I am trying to do PCA analysis for my samples for initial quality control. I have 2 different sets of samples - one were sequenced 50bp and other was sequenced 75bp (both of them have disease and control cases). To do the PCA on those samples, I ran DEseq2 on them (which necessarily requires non-normalized counts), followed by vst and plotPCA. But in my PCA plot, I see two clusters - one for the 50bp samples and the other for 75 bp samples. This is not necessarily expected, since there is nothing different between the samples except for sequencing depth. Someone said I should normalize my data. But I think that will be taken care of by DESeq2, and it anyway shouldn't be fed normalized counts. Here is the plot.

Any suggestions? PCA plot link

Here is the image link in case it doesn't show - https://imgur.com/CFXHky4

deseq2 PCA • 180 views
ADD COMMENT
0
Entering edit mode
@kevin
Last seen 55 minutes ago
Republic of Ireland

Cross-posted and answered on Biostars: https://www.biostars.org/p/434664/

ADD COMMENT

Login before adding your answer.

Traffic: 446 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