DESeq2 log fold change
2
0
Entering edit mode
bioinfo • 0
@bioinfo-12782
Last seen 19 months ago
United States

Dear DESeq2 developer and colleagues,

DESeq2 generates an output table including "log2FoldChange". I have two questions about this value.

I. As far as I know, this is a moderated version, not a log2 fold change from the raw count value. But I want to have unmoderated value that can be calculated from count directly and my current way is: (1) get normalized count (2) log transformation (3) calculate averages per condition (4) divide two averages: "FC". Is this a right way? I am confusing whether it is fold change of log, or log of fold change.

II. Effect size is "log2FoldChange" divided by SD where SD is sqrt(1/mu + dispersion). Here, I think that mu is an average of "log" of normalized count and dispersion can be retrieved by a command "dispersions()". I assume that this command outputs in a same order with "results()" to match values between two output objects. Also, I can use moderated version or unmoderated version with the same formula, mu and dispersion. Are they correct ?

deseq2 • 841 views
ADD COMMENT
0
Entering edit mode
swbarnes2 ★ 1.3k
@swbarnes2-14086
Last seen 17 hours ago
San Diego

1) get normalized count (2) log transformation (3) calculate averages per condition (4) divide two averages: "FC". Is this a right way?

No. Take the averages of the normalized counts, divide one by the other, take the log base 2 of that.

ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 9 hours ago
United States

DESeq() since version 1.15 (~2.5 years) has not performed shrinkage, but this was moved to lfcShrink(), see the current vignette.

The standard deviation of the LFC is not equal to sqrt(1/mu + dispersion). See the DESeq2 paper for details.

ADD COMMENT
0
Entering edit mode

Thanks for your answer. I saw your post a long time ago: https://www.biostars.org/p/140976/ So was this changed?

ADD REPLY
0
Entering edit mode

Yes, as I said, and you can read about it in the vignette.

ADD REPLY

Login before adding your answer.

Traffic: 637 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