[BioC] question on easyRNASeq developer version

Nicolas Delhomme delhomme at embl.de
Thu Sep 20 15:06:28 CEST 2012

Dear René,

The best place to post this - where you would get for sure my attention - is the bioconductor mailing list. The advantage is that other developers/users might be able to help you as your message would have a better visibility to the R/Bioc community. I've actually put that mailing list in Cc.

There indeed seem to be a sub-setting error somewhere within the function that parses the read information, or so I guess from your error message. Would it be possible for you to share your EMC_18_alignment.bam file? I can set up a folder in my dropbox for you to upload the file. If that is not possible, can you at least trim your bam file to the smallest size sufficient to reproduce the error and share that excerpt with me?



Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany

On Sep 20, 2012, at 2:04 PM, René Böttcher wrote:

> Dear Mr. Delhomme,
> I would like to ask for your support concerning a problem I'm facing when using your easyRNASeq package. There seems to be an issue in one of the subfunctions, 
> however, I am not able to tell which one, as the error message is rather short.
> "Error in mk_singleBracketReplacementValue(x, value) : 
> 'value' must be a CompressedIntegerList object"
> Please not that I'm trying to follow the example cases you provided and I am currently using the developer version since my alignments require multiple reads length support according to your current stable release. You can find a detailed problem description on Seqanswers, as it seems I am not the only one encountering this problem.
> http://seqanswers.com/forums/showthread.php?t=23477
> With kind regards,
> René Böttcher

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