Question: plotMA (DESeq2) Issue
0
gravatar for ap_vc21
16 months ago by
ap_vc210
ap_vc210 wrote:

I am following the standard RNA-seq analysis workflow to make sense of some experimental data, using the DESeq2 package. Here is the MA-plot I have:

I am not concerned about the low log-fold change, but this looks a bit weird, since I would have expected the major part of the genes to be found in the low counts range.

I followed the standard pipeline for this analysis. Is there any obvious reason why I am having this kind of result?

Thank you.

ADD COMMENTlink modified 16 months ago by Michael Love24k • written 16 months ago by ap_vc210
Answer: plotMA (DESeq2) Issue
1
gravatar for Michael Love
16 months ago by
Michael Love24k
United States
Michael Love24k wrote:

Sorry, what is not expected here? DESeq2 moderates the LFC from genes with little to no information for accurately estimating the LFC. Please see the DESeq2 paper or the vignette section on LFC shrinkage.

ADD COMMENTlink written 16 months ago by Michael Love24k

I am quite new to the field, so I am very open to be totally mistaken. The shrinkage in the LFC in the low counts range has to considered as normal then? 

ADD REPLYlink written 16 months ago by ap_vc210

Take a look at the paper and the vignette. You will find the same kind of plots there. Again, it is expected.

ADD REPLYlink written 16 months ago by Michael Love24k
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 16.09
Traffic: 159 users visited in the last hour