[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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