This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What means negative values in LogCPM Smear Plot - edgeR ?

Hi, I am trying to figure out why I'm getting negative values in LogCPM in SmearPlot of edgeR. LogCPM isn't an intensity mean? How could be less than 0?

My count files seems to be fine.

plot image

I can post the R script if necessary. Thanks very much until now.

edger rna-seq r maplot smear
• 9,831 views • link
updated by qiz218591 • qiz218591 • written by rodolpho.gheleri • rodolpho.gheleri

2 answers

Any CPM < 1 will be negative...

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan
Now I understand. But there is a norm or something like it that I can do to keep >= 0?
• 0 views • link
written by rodolpho.gheleri • rodolpho.gheleri

No, then they wouldn't be CPMs. You'll need to subset the data if for some reason you require logCPM to be >=0.

• 0 views • link
written by Devon Ryan Devon Ryan

Why the logcpm should be greater than equal to zero?? If log cpm is negative then it might be the possibility of having the some genes with low expression levels right? Please do correct me if i am wrong.

• 0 views • link
written by qiz218591 • qiz218591

Log in to answer this question.

More posts like this