Hi Cass, Thank you very much for the valuable feedback! Yes, the function expects peak.ranges to be a RangedData with a "names" field as the name of the binding site. I will add your fix to make sure the function works when "names" field is not set. Thanks again for making this package more user friendly! Best regards, Julie ******************************************* Julie Zhu, Ph.D Research Associate Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 508-856-5256 http://www.umassmed.edu/pgfe/faculty/zhu.cfm On 1/14/10 7:41 AM, "Cass Johnston" <caroline.johnston at="" kcl.ac.uk=""> wrote: > Hello, > > I'm getting an error from ChIPpeakAnnot when I try and get the nearest > TSS to a load of ChIPseq peaks: > > annotatedPeak = annotatePeakInBatch(peak.ranges[1:5,], AnnotationData = > TSS.mouse.NCBIM37) > Error in dimnames(x) <- dn : > length of 'dimnames' [2] not equal to array extent > > Giving the peaks default rownames seems to fix it: > > *** annotatePeakInBatch.R.old 2010-01-14 12:36:00.000000000 +0000 > --- annotatePeakInBatch.R 2010-01-14 12:37:47.000000000 +0000 > *************** > *** 26,31 **** > --- 26,34 ---- > "strand") > allChr.Anno = unique(space(TSS.ordered)) > numberOfChromosome = length(unique(space(myPeakList))) > + if(is.null(rownames(myPeakList))){ > + rownames(myPeakList)<-paste("peak", seq(1,nrow(myPeakList)), > sep="") > + } > z1 = cbind(as.character(rownames(myPeakList)), > as.character(space(myPeakList)), > start(myPeakList), end(myPeakList)) > colnames(z1) = c("name", "chr", "peakStart", "peakEnd") > > > Cheers, > Cass Johnston. > >