Question: lfcShrink in DESeq2
0
gravatar for Meghdad
13 days ago by
Meghdad0
Meghdad0 wrote:

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 • 89 views
ADD COMMENTlink modified 13 days ago by Michael Love24k • written 13 days ago by Meghdad0
Answer: lfcShrink in DESeq2
0
gravatar for Michael Love
13 days ago by
Michael Love24k
United States
Michael Love24k wrote:

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 COMMENTlink written 13 days ago by Michael Love24k

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 REPLYlink written 12 days ago by Meghdad0
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