Multiple issues reading in peak sets with Diffbind
Entering edit mode
os306 • 0
Last seen 8 weeks ago
United States


I am pulling my hair out trying to figure out how to resolve an issue I am having with reading peaksets into Diffbind. The peaks files I am trying to use are .narrowPeak files derived from MACS2. It is my understanding that Diffbind is able to read these .narrowPeak files if one specifies "narrow" in the PeakCaller column. Despite doing this, and following the instructions for creating the sample sheet word for word, I am receiving the following error when I type in the code below:


"Error in peaks[, pCol]/max(peaks[, pCol]) : 
  non-numeric argument to binary operator"

I have no "scoreCol" column in my sample sheet. I wondered whether maybe Diffbind was having trouble with the .narowPeak files so substituted these files for the .xls MACS2 outputs (and changed the PeakCaller column content to "macs2". However, now I receive the following error:

"Error in read.table(fn, blank.lines.skip = TRUE, header = TRUE) : 
  more columns than column names"

I am confused as to why I am getting these errors and would be grateful for any guidance.

DiffBind • 226 views
Entering edit mode

I have also had this problem today with a sample sheet that appears to be just like another sheet I previously used. I also had narrow as the peakCaller. Interested to hear answers!

Entering edit mode
Rory Stark ★ 4.9k
Last seen 8 hours ago
CRUK, Cambridge, UK

It helps if you include the software versions you are using (output of sessionInfo()).

If you could send me a copy of one of your peak files (or just the first 30 lines or so) I can have a look at what is going on.


Login before adding your answer.

Traffic: 230 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6