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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ 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 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}