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:
res=dba(sampleSheet=samples) "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.
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!