[BioC] Writing table from DGEExact object (edgeR)

[Mark Robinson]

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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