[BioC] easyRNAseq and DEseq for no replicate RNAseq

[Nicolas Delhomme]

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$")
cds <- easyRNASeq(filesDirectory=system.file("extdata",package="RnaSeqTutorial"),
                            pattern="[A,C,T,G]{6}\\.bam$",readLength=30L,
                            organism="Dmelanogaster",annotationMethod="gff",
                            annotationFile=system.file("extdata","annot.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
Umeå Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

On 26 Nov 2013, at 10:30, Isabelle Stévant <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 Stévant, PhD Student
> Department of Genetic Medicine and Development
> University of Geneva Medical School
> 1, rue Michel-Servet
> CH 1211 Geneva 4 Switzerland
> 
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