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Issues with DiffBind

I just started (trying) using DiffBind and I've gotten stuck on literally the first step.

I've written a sampleSheet and saved it as a txt file and then tried to load it using the code Polycomb = dba(sampleSheet=Polycomb.txt (also tried it as CSV and didn't work).

I keep getting back this message and can't seem to resolve it even though I've read all the previous threads.

Error in if (is.na(peaks)) { : argument is of length zero

Any help would be much appreciated,

Thanks
Val

chip-seq diffbind
• 4,428 views • link
updated by Ram Ram • written by V V

1 answer

Hi Val,

Make sure your header in the sample sheet is right. Looks like your Peak column cannot be found. Here is how my header looks like:

SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks,PeakCaller,ControlID

Pascal

• 0 views • link
updated by Ram Ram • written by Pascal Pascal

Hi

Thanks for the help, I've changed all my columns to mirror what you've written above but still getting the same thing.

Maybe its how I filled out the columns ? Can't think of anything else

Val

• 0 views • link
updated by Ram Ram • written by V V

Try opening the file in excel/csv viewer and make sure your columns are matching up correctly

• 0 views • link
updated by Ram Ram • written by Ying W Ying W

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