Combining VST counts for replicates
1
0
Entering edit mode
@49806f54
Last seen 1 day ago
United States

I performed variance stabilized transformation on raw gene counts. Now for the future purpose, I want to combine replicates and calculate the log fold change values between control and experimental condition (I don't want to perform differential expression analysis). How can I combine the VST counts? I tried combining them by mean() which is basically geometric mean as the values are in log. But I noticed that log fold change distribution is drastically shifted (from zero) for some experimental conditions with lot of replicates (more than 2). Any suggestions?

DESeq2 • 78 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 4 hours ago
United States

We recommend using original counts for computing LFC (discussed in workflow).

ADD COMMENT

Login before adding your answer.

Traffic: 514 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