This is a question on the dba.report function in DiffBind.

I am trying to retrieve all sites (including non-differential and differential sites) by using the following script:

GRanges.steady <- dba.report(diff.analysis.steady, method=DBA_DESEQ2_BLOCK, th=1, bUsePval=FALSE)

However, the following error message was returned:

Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 

  solving row 14834: range cannot be determined from the supplied arguments (too many NAs)

Calls: dba.report ... newGRanges -> IRanges -> solveUserSEW0 -> .Call2 -> .Call

The above script worked fine if th=0.1 is used. 

Presumably, this is because some of the sites have "NA" in their adjusted p-value column from DESeq2, but I do not know how to circumvent this problem with the dba.report function to retrieve all the sites.

I would appreciate any suggestions on this.

My DiffBind version is 1.12.0

Thanks,

Mei San

Hello Mei San-

The best way for me to figure this out is if I could get access to your DBA object diff.analysis.steady, could you send me a copy in email (or a download link)?

Cheers-

Rory

rory.stark@cruk.cam.ac.uk

Hi Mei San-

Thanks for sending me your objects. I was able to identify a bug in the calculation of summit locations that resulted in some divide-by-zeroes, hence the problem with NAs. I've checked in a fix that will appear in DiffBind 1.14.1 in the next few days. Let me know if there is still a problem with that version.

Cheers-

Rory