Question: Subset DEG from Deseq2-use padj from results() or lfcShrink()?
0
gravatar for s.l.lee
8 months ago by
s.l.lee20
s.l.lee20 wrote:

Hi all,

I am doing RNAseq analysis for DEG using Deseq2 package. I am trying to subset my list of DEG using both padj value and log2FC. I have analysed my results using the Deseq() function and extracted the results using results(). I have also shrunken my Log2FC using lfcShrink().

My question is simply, when I am subseting my list of DEG, should I used the padj values from results() or lfcShrink(), as they are different. (I will be using the log2FC results from lfcShrink). I have read that performing the lfcShrink() function shouldnt change the list of DEG but obviously the list will change if I use the padj from lfcShrink().

Is the padj from lfcShrink a more reliable value or is it just a more conservative method? Thank you.

rna-seq deseq2 • 381 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by s.l.lee20
3
gravatar for ATpoint
8 months ago by
ATpoint44k
ATpoint44k wrote:

If you set contrasts/coefficients properly the results should/must be the same in terms of p-values since the function adds shrunken fold changes, it does not recompute significances. Please show code.

ADD COMMENTlink modified 8 months ago • written 8 months ago by ATpoint44k

I think I figured out what the problem was: Myalpha was set at 0.05 for results()

My initial code for results() was:

res<-results(dds,alpha= 0.05)

and for lfcShrink():

lfcres<-lfcShrink(dds,coef=2,type="apeglm",res=res)

The above code gave me different padj values. However, when I changed my results() code to:

res<-results(dds,alpha= 0.1)

The padj values were the same for both. Is there an option to set lfcShrink() to alpha=0.05?

Thank you.

ADD REPLYlink written 8 months ago by s.l.lee20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1359 users visited in the last hour
_