[BioC] easyRNAseq and DEseq for no replicate RNAseq

Isabelle Stévant isabelle.stevant at gmail.com
Tue Nov 26 10:30:15 CET 2013


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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