Unusual distribution of LogFC in EdgeR (Single cell)
I am doing a differential expression analysis using single cell analysis using edgeR and getting skewed distribution of LogFC. Any thoughts on why I am getting the following distribution.
The code for the analysis
dge <- calcNormFactors(dge)
design <- model.matrix(~0+group, data=dge$samples)
dge <- estimateDisp(dge, design = design)
fit <- glmQLFit(dge, design = design)
my.contrasts <- makeContrasts(KO_vs_WT = groupKO-groupWT, levels=design)
qlf.contrast <- glmQLFTest(fit, contrast=my.contrasts)
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rpolicastro
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kvshamsudheen
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kvshamsudheen
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Can you describe in more detail how you are doing the analysis, and possibly include your code?
Here is the scripts and analysis description.