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

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. Thanks, Nico --------------------------------------------------------------- Nicolas Delhomme Nathaniel Street Lab Department of Plant Physiology Ume? Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delhomme at plantphys.umu.se SLU - Ume? universitet Ume? 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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor