lfcShrink in DESeq2
1
0
Entering edit mode
Meghdad • 0
@meghdad-21558
Last seen 2.1 years ago

Dear all,

I am new to RNA seq data analysis. I have been trying to do some DE analysis using DESeq2. I am comparing two conditions, and I expect two genes X and Y to differ in these conditions. When I put condition 1 as reference, the MA plot looks as figure A, and when I do lfcShrink using apeglm, it looks like figure B, my genes of interests still there. When I put condition 2 as reference, the MA plot is the figure C. However, this time after shrinkage (figure D), the lfc of one of my genes of interest goes to almost zero. Can you please clarify why this is happening? Best![enter image description here][2]

Figure

deseq2 apeglm • 503 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 6 hours ago
United States

I think that the adaptive prior of apeglm is not working well for this dataset. It looks like you have many genes consistent with LFC=0 and then two very large effects. Obviously, this is the kind of situation we were trying to accommodate when developing apeglm, but we use a Cauchy prior, and it looks like this needs a prior with even more extreme "kurtosis" (more of a spike and slab shape). Can you try type="ashr", which fits a flexible mixture prior?

ADD COMMENT
0
Entering edit mode

Dear Michael,

Thanks a lot for your reply. I tried with type="ashr", and as can be seen in FigureE, the lfc of genes X and Y are preserved.

ADD REPLY

Login before adding your answer.

Traffic: 336 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