Hi thanks for your reply, but I've actually worked out that this problem was to do with the fact that i was running an older version of Bioconductor. Version 2.5.1. Upgrading has solved it. Sorry for wasting your time. -Paul On Mon, Apr 7, 2008 at 8:40 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > Hi Paul -- can you please provide the output of sessionInfo() ? > > Thanks, > > Martin > > > > "Paul Geeleher" <paulgeeleher at="" gmail.com=""> writes: > > > Dear Memebers, > > > > I want to be able to reference individual arrays in an abatch like so > > abatch[,1], abatch[,2] etc. > > > > This seems to work fine using the original pData for the abatch after > > using ReadAffy(): > > > > sample > > N10S.CEL 1 > > N11S.CEL 2 > > N12S.CEL 3 > > N7S.CEL 4 > > N8S.CEL 5 > > N9S.CEL 6 > > P1S.CEL 7 > > P2S.CEL 8 > > P3S.CEL 9 > > P4S.CEL 10 > > P5S.CEL 11 > > P6S.CEL 12 > > > > > > But when I run these commands: > > > > pd <- data.frame(population = c(1,1,1,1,1,1,2,2,2,2,2,2), replicate = > > c(1,2,3,4,5,6,1,2,3,4,5,6), sample = c(1,2,3,4,5,6,7,8,9,10,11,12)) > > rownames(pd) <- sampleNames(abatch) > > pData(abatch) <- pd > > > > Which changes the pData for the abatch to this: > > > > population replicate sample > > N10S.CEL 1 1 1 > > N11S.CEL 1 2 2 > > N12S.CEL 1 3 3 > > N7S.CEL 1 4 4 > > N8S.CEL 1 5 5 > > N9S.CEL 1 6 6 > > P1S.CEL 2 1 7 > > P2S.CEL 2 2 8 > > P3S.CEL 2 3 9 > > P4S.CEL 2 4 10 > > P5S.CEL 2 5 11 > > P6S.CEL 2 6 12 > > > > Referencing the arrays using "abatch[,1]" throws up the following error: > > > > Error in `row.names<-.data.frame`(`*tmp*`, value = c("sample", "population", : > > invalid 'row.names' length > > > > > > How can I change the pData and still be able to reference the arrays > > like "abatch[,1]"? > > > > Thanks, > > -Paul > > > > _______________________________________________ > > 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 > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 >