What means negative values in LogCPM Smear Plot - edgeR ?

Question

[rodolpho.gheleri]

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.

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

Answer 1

[Devon Ryan]

Any CPM < 1 will be negative...

[rodolpho.gheleri]

Now I understand. But there is a norm or something like it that I can do to keep >= 0?

[Devon Ryan]

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

Answer 2

[qiz218591]

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.