Unusual distribution of LogFC in EdgeR (Single cell)

0

Entering edit mode

3.3 years ago

kvshamsudheen ▴ 120

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. LogFold change plot

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)

EdgeR Differential expression RNA-Seq • 1.1k views

ADD COMMENT • link updated 3.2 years ago by rpolicastro 13k • written 3.3 years ago by kvshamsudheen ▴ 120

0

Entering edit mode

Can you describe in more detail how you are doing the analysis, and possibly include your code?

ADD REPLY • link 3.3 years ago by rpolicastro 13k

0

Entering edit mode

Here is the scripts and analysis description.

ADD REPLY • link 3.3 years ago by kvshamsudheen ▴ 120

Login before adding your answer.