LFCshrink function understanding
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evelas13 • 0
Last seen 2.7 years ago

Hello i'm kind of new to RNA-seq. I'm tryin to make a DE analysis using DEseq2 and i tried to read and understand the function of lfcshrink. So i tried using MAplots to help me understand. The problem is that in the MAplot there are several points(genes) that are above the lfc threshhold and are painted bliue in the MA plot but when i do the summary they don't appear. Here are the lines and images:

  • -ddscollapsed <- DESeq(ddscollapsed)
  • res <- results(ddscollapsed, contrast = c('condition', 'ocho', 'seis')coefi<-resultsNames(ddscollapsed)
  • lfcutoff<-0.7
  • res.lfc2 <- lfcShrink(ddscollapsed, coef= coefi[2], type="apeglm",lfcThreshold = lfcutoff)
  • plotMA(res.lfc2, ylim=c(-2,2), main="apeglm, LFC 6vs8", alpha=0.05)
  • abline(h=c(-lfcutoff,lfcutoff), col="dodgerblue", lwd=2)
  • summary(res.lfc2)

The output of this is: out of 11247 with nonzero total read count s-value < 0.005

  • LFC > 0.70 (up) : 0, 0%
  • LFC < -0.70 (down) : 8, 0.071%

The plot is:enter link description here:MAplot,0.7 TH

┬┐Is it because the graph is showing like the mean lfcthreshold and is not actually the same as the threshhold i input?

Thanks for your help and time

deseq2 MAplot lfcshrink • 465 views
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Last seen 8 days ago
United States

The cutoff on svalue is 0.005 in the summary and 0.05 in the MA plot.


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