[BioC] Devel version of easyRNASeq: using the simpleRNASeq method gives an error

Nicolas Delhomme nicolas.delhomme at umu.se
Thu Mar 27 15:05:42 CET 2014

Hej Sylvain!

Indeed that function is under very active development and I’ve broken it times and again :-)

I would suggest you to keep using the easyRNASeq function until the next Bioc release (planned in ~10 days). I’m rushing to get the simpleRNASeq in the next release as bug-free as possible and I expect it to be fairly unstable by then.

Anyway, can you tell me which easyRNASeq version you are using (run sessionInfo() or package.version(“easyRNASeq”) in your R session)? Just so that I make sure I’ve got that bug squashed already.



Nicolas Delhomme

Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 5478
Email: nicolas.delhomme at plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden

On 27 Mar 2014, at 14:40, Sylvain Foisy Ph. D. <sylvain.foisy at diploide.net> wrote:

> Hi to all,
> I am trying to use the R-devel branch for easyRNASeq to get gene counts from filtered BAM files and I get the following error:
>> exp<-simpleRNASeq(bamFiles = bfl, param = rParam, nnodes = 1, verbose = TRUE)
> Error in (function (classes, fdef, mtable)  : 
>  unable to find an inherited method for function ‘simpleRNASeq’ for signature ‘"BamFileList”’
> According to the help material, simpleRNASeq should need this:
>     simpleRNASeq(bamFiles = BamFileList(),
>       param = RnaSeqParam(), nnodes = 1, verbose = FALSE)
> When I check the nature of my bfl object, I get this:
>> bfl
> BamFileList of length 103
> names(103): 123456_CELLTYPE_B_accepted_hits_properly_paired.bam …
> So bfl is the right type… Any ideas or is this a bug? It’s the devel version after all ;-)
> Best regards
> S
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