Question: LRT test in DESeq2 gives weird volcano plot
gravatar for EVR
11 months ago by
EVR570 wrote:

Dear All,

I am using LRT(with full model and reduced model) to compute the differential expressed genes. But when I generate the volcanoplot using ggplot, I am getting the following figure where point converged towards the summit. I also came across similar plot in bioconductor forum when LRT was used in DESeq2. Also the number of differential expressed genes for

padj <0.05 & abs(Log2foldchange) >1=60

whereas for

padj <0.05 & abs(Log2foldchange) > 0.5 = 265

Why is this so vast difference?

Kindly guide me

lrt rna-seq volcanoplot deseq2 • 333 views
ADD COMMENTlink modified 11 months ago by ATpoint36k • written 11 months ago by EVR570

ADD REPLYlink written 11 months ago by EVR570

Please add relevant code and embed images properly How to add images to a Biostars post

ADD REPLYlink modified 11 months ago • written 11 months ago by ATpoint36k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 964 users visited in the last hour