Question: LRT test in DESeq2 gives weird volcano plot
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gravatar for EVR
12 days ago by
EVR560
Earth
EVR560 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

https://drive.google.com/open?id=17a9st9esiDvoDzD6H5VAo-jYytvMyQ6r

lrt rna-seq volcanoplot deseq2 • 64 views
ADD COMMENTlink modified 12 days ago by ATpoint23k • written 12 days ago by EVR560

https://drive.google.com/open?id=17a9st9esiDvoDzD6H5VAo-jYytvMyQ6r

ADD REPLYlink written 12 days ago by EVR560

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

ADD REPLYlink modified 12 days ago • written 12 days ago by ATpoint23k
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