Question: Problem with low count removal in edgeR ?
0
gravatar for Björn
20 months ago by
Björn40
Björn40 wrote:

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

ADD COMMENTlink written 20 months ago by Björn40

Show how you got cpm and an example of a row with all 0 counts.

ADD REPLYlink written 20 months ago by Devon Ryan95k

I followed the paper literature

and after this step

o<-order(qlfGrAvsGrB$table$PValue)
cpm(y)[o[1:25],]

produces list of miRNAs "with zero" counts. See attached file. The row numbers are ID for miRNAs. while each column represents sample. figure

ADD REPLYlink modified 20 months ago by Devon Ryan95k • written 20 months ago by Björn40

Those rows aren't all zeros.

ADD REPLYlink written 20 months ago by Devon Ryan95k

My concern is why there is still zero counts (in some samples)?

ADD REPLYlink modified 20 months ago • written 20 months ago by Björn40

Because they should be there. The remove.zeros option isn't doing what you think it is.

ADD REPLYlink written 20 months ago by Devon Ryan95k

Is it really a problem after using

keep<-rowSums(cpm>1)>=6
table(keep)
ADD REPLYlink written 20 months ago by Björn40

Obviously it is.

ADD REPLYlink written 20 months ago by Devon Ryan95k

I believe those with counts below 1 CPM (which includes 0) will be excluded in "keep" so why it is still a problem.

ADD REPLYlink written 20 months ago by Björn40

It's unclear if you're actually using keep or if >=6 is sufficient. As an aside, it's questionable whether you actually want to do this.

ADD REPLYlink written 20 months ago by Devon Ryan95k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1235 users visited in the last hour