LRT test in DESeq2 gives weird volcano plot
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
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