[BioC] Writing table from DGEExact object (edgeR)
Mark Robinson
mrobinson at wehi.EDU.AU
Mon Nov 22 19:29:38 CET 2010
Hi Karen.
Try:
[...]
de <- exactTest(d)
write.table(de$table, "file.txt", sep="\t", ...)
Cheers,
Mark
On 2010-11-20, at 5:35 AM, Karen Sherwood wrote:
> Dear All,
>
> I would appreciate some help with writing a table out from a DGEExact
> object. I have used edgeR to produce an DGEExact output table. The data
> frame contains the log-concentration (i.e. expression level), the log-fold
> change in expression between the two groups/conditions and the p-value for
> differential expression as columns and many several thousand rows (from
> high-throughput sequencing data). I would like to know how to write.table
> this object.
> If I write.table (object name,"file.txt",sep-"\t",col.names=NA), the error
> is returned
>
> Error in data.frame(table=list(logConc=c(),: arguments imply differing
> number of rows:18314,2,0
>
> I have tried sink, write.csv and write.foreign from package foreign but I am
> unable to write the object out.
>
> Any suggestions would be greatfully received,
> Thank you,
> karen
>
>
>
> Dr. Karen Sherwood
> College of Medicine and Veterinary Medicine
> Laboratory for Clinical and Molecular Virology,
> The Roslin Institute, Centre for Infectious Diseases, R(D)SVS,
> University of Edinburgh
> Summerhall, Edinburgh EH9 1QH, UK
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobinson at wehi.edu.au
e: m.robinson at garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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