Problem with low count removal in edgeR ?
I used following command to remove zero counts using edgeR package
y<-DGEList(data, genes = miRNAs_ID,group = diagnostics, remove.zeros = T)
which removed nearly 1000 miRNA (rows) from subsequent "y" that is used for analysis. Following command to exclude low counts was
keep<-rowSums(cpm>1)>=6
table(keep)
This left 600 miRNAs (rows). However, using commandline
cpm(y)[o[1:25],]
to list first 25 rows of miRNAs still shows those with zero counts. The above command was used after using threshold of CPM of 1. What is wrong with it ? I would suppose that the "y" should not contain any miRNAs with "0". Thanks
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Show how you got
cpmand an example of a row with all 0 counts.I followed the paper literature
and after this step
produces list of miRNAs "with zero" counts. See attached file. The row numbers are ID for miRNAs. while each column represents sample.
Those rows aren't all zeros.
My concern is why there is still zero counts (in some samples)?
Because they should be there. The
remove.zerosoption isn't doing what you think it is.Is it really a problem after using
Obviously it is.
I believe those with counts below 1 CPM (which includes 0) will be excluded in "keep" so why it is still a problem.
It's unclear if you're actually using
keepor if>=6is sufficient. As an aside, it's questionable whether you actually want to do this.