[BioC] easyRNAseq and DEseq for no replicate RNAseq

[Nicolas Delhomme]

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 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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---------------------------------------------------------------
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