Hi, I am trying to process sereral RNAseq using easyRNAseq package but I am facing an error I don't manage to fix. I use R version 3.0.2, and easyRNAseq version 1.8.2. I have 45 RNAseq with no replicates. I use this to call easyRNAseq, as described in the documentation: count.table <- easyRNASeq(filesDirectory= "/path/to/bamFiles", format="bam", pattern="*.bam$", readLength=50L, annotationMethod="gtf", annotationFile="/path/to/Mus_musculus.GRCm38.73_cleaned.gtf", count="exons", outputFormat="DESeq", normalize=TRUE, conditions=conditions, fitType="local", method="blind" ) I get this error: Checking arguments... Fetching annotations... Error in fetchAnnotation(obj, method = annotationMethod, filename = annotationFile, : formal argument "method" matched by multiple actual arguments Calls: easyRNASeq -> easyRNASeq -> fetchAnnotation Does the keyword "method" have changed or did I missed something? Thanks, Isabelle -- Isabelle St?vant, PhD Student Department of Genetic Medicine and Development University of Geneva Medical School 1, rue Michel-Servet CH 1211 Geneva 4 Switzerland

Hej Isabelle! There may indeed have been a change in an internal function that may affecting this. I?ll take a look and come back to you asap. Cheers, Nico --------------------------------------------------------------- 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 26 Nov 2013, at 10:30, Isabelle St?vant <isabelle.stevant at="" gmail.com=""> wrote: > Hi, > > I am trying to process sereral RNAseq using easyRNAseq package but I > am facing an error I don't manage to fix. > > I use R version 3.0.2, and easyRNAseq version 1.8.2. > > I have 45 RNAseq with no replicates. I use this to call easyRNAseq, as > described in the documentation: > > count.table <- easyRNASeq(filesDirectory= "/path/to/bamFiles", > format="bam", > pattern="*.bam$", > readLength=50L, > annotationMethod="gtf", > > annotationFile="/path/to/Mus_musculus.GRCm38.73_cleaned.gtf", > count="exons", > outputFormat="DESeq", > normalize=TRUE, > conditions=conditions, > fitType="local", > method="blind" > ) > > > I get this error: > > Checking arguments... > Fetching annotations... > Error in fetchAnnotation(obj, method = annotationMethod, filename = > annotationFile, : > formal argument "method" matched by multiple actual arguments > Calls: easyRNASeq -> easyRNASeq -> fetchAnnotation > > Does the keyword "method" have changed or did I missed something? > > > Thanks, > Isabelle > > -- > Isabelle St?vant, PhD Student > Department of Genetic Medicine and Development > University of Geneva Medical School > 1, rue Michel-Servet > CH 1211 Geneva 4 Switzerland > > _______________________________________________ > 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 --------------------------------------------------------------- Nicolas Delhomme Nathaniel Street Lab Department of Plant Physiology Ume? Plant Science Center Tel: +46 90 786 7989 Email: nicolas.delhomme at plantphys.umu.se SLU - Ume? universitet Ume? S-901 87 Sweden

Hej Isabelle! This was due to the argument named ?method" colliding with another similarly named argument of an internal function of easyRNASeq. This is fixed in version 1.8.3 that should be available over the WE or now if your are using SVN. For the record, here is how I reproduced your error: library(easyRNASeq) library(RnaSeqTutorial) conditions <- rep(c("C","T"),2) names(conditions) <- dir(system.file("extdata",package="RnaSeqTutorial "),pattern="[A,C,T,G]{6}\\.bam$") cds <- easyRNASeq(filesDirectory=system.file("extdata",package="RnaSeq Tutorial"), pattern="[A,C,T,G]{6}\\.bam$",readLength=30L, organism="Dmelanogaster",annotationMethod="gff", annotationFile=system.file("extdata","anno t.gff",package="RnaSeqTutorial"), count="exons",outputFormat="DESeq",method="blind",fitType="local", normalize=TRUE, conditions=conditions) This does now work in version 1.8.3. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Nathaniel Street Lab Department of Plant Physiology Ume? Plant Science Center Tel: +46 90 786 7989 Email: nicolas.delhomme at plantphys.umu.se SLU - Ume? universitet Ume? S-901 87 Sweden --------------------------------------------------------------- On 26 Nov 2013, at 10:30, Isabelle St?vant <isabelle.stevant at="" gmail.com=""> wrote: > Hi, > > I am trying to process sereral RNAseq using easyRNAseq package but I > am facing an error I don't manage to fix. > > I use R version 3.0.2, and easyRNAseq version 1.8.2. > > I have 45 RNAseq with no replicates. I use this to call easyRNAseq, as > described in the documentation: > > count.table <- easyRNASeq(filesDirectory= "/path/to/bamFiles", > format="bam", > pattern="*.bam$", > readLength=50L, > annotationMethod="gtf", > > annotationFile="/path/to/Mus_musculus.GRCm38.73_cleaned.gtf", > count="exons", > outputFormat="DESeq", > normalize=TRUE, > conditions=conditions, > fitType="local", > method="blind" > ) > > > I get this error: > > Checking arguments... > Fetching annotations... > Error in fetchAnnotation(obj, method = annotationMethod, filename = > annotationFile, : > formal argument "method" matched by multiple actual arguments > Calls: easyRNASeq -> easyRNASeq -> fetchAnnotation > > Does the keyword "method" have changed or did I missed something? > > > Thanks, > Isabelle > > -- > Isabelle St?vant, PhD Student > Department of Genetic Medicine and Development > University of Geneva Medical School > 1, rue Michel-Servet > CH 1211 Geneva 4 Switzerland > > _______________________________________________ > 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