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Hello,
I am analyzing some ChIP-seq data with Diffbind, and everything works great until when I was trying to use its plotprofile funtion. The command and error messages are attached below. Since I was using Ensembl GRCh38.p13 as the reference genome, I guess this arises from the format of chromosome numbers? However, I am unexperienced with R, and have no idea how to solve the problem. I really appreciate if anyone can help!
profiles <- dba.plotProfile(Ezh2.MAPQ20)
Generating report-based DBA object...
Generating profiles...
Error in value[[3L]](cond) :
profileplyr error: Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6
first error: BiocParallel errors
element index: 1
first error: different row counts implied by arguments
In addition: Warning message:
In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Hi there, it's hard to tell how to debug without having the data. Could you potentially send me the object you are attempting to use for this function call? In case you haven't done this before, you can just do 'saveRDS(object, "filepath/object.rds")'. It would also be helpful if you posted your session info (type sessionInfo() into RStudio) to account for software versions when trying to reproduce the error.
You can email it to me doug[period]barrows[at]gmail[period]com
Thank you for your reply! I have sent the RDS object and session info to your email!
In case anyone else encounters this problem, there was a bug in profileplyr (used by the dba.plotProfile() function in DiffBind) when the BAM files were made using the Ensembl reference genome. This has been fixed in the current Bioconductor v3.13 release of the package (v 1.8.1), so updating profileplyr and reloading DiffBind should fix it.