Hello All, Another problem has come up that hopefully someone can provide some assistance with... I am trying to plot ChIP data in relation to the TSS as show in the Starr vignette but the following error comes up when I call the getProfiles function: > profile = getProfiles(wtNucRatio, probeAnnot, tssAnno, 800, 800, feature = "TSS", borderNames = "TSS", method = "basewise") chromosome NA Error in probeAnno[paste(chr[i], "index", sep = ".")] : No mapping 'NA.index' in this 'probeAnno' object. My particular probeAnno object (probeAnnot) was created using both functions recommended on this board and in the vignette. For example: using the Ringo function of: posToProbeAnno > probeAnnot <- posToProbeAnno(pos, genome="Saccer", microarrayPlatform = "Affymetrix") or the Starr function of bpmapToProbeAnno > probeAnno = bpmapToProbeAnno(bpmap) both methods print out the probeAnno mapping for chromosome and do not throw any errors so I assumed the object was made correctly. So I think the error above may be coming from elsewhere but I cannot find it and do not know how to fix it. Any help would be greatly appreciated. PS. I created the tssAnno using biomaRt and everything in that looks to be okay... noah

Dear Noah thank you. Please next time do remember to mention the output of "sessionInfo()" in your post and to provide a reproducible example. By making it easier for others to help you, you increase the chance of them doing it. In this case, I cannot reproduce your example because I do not have the files that you use. Anyway, what do you get when you type: ls(probeAnnot) head(tssAnno) It appears (from what I can tell) that your tssAnno data frame contains "NA" values in the chromosome name column, and quite justifiably the "getProfiles" function is not happy with that. Try removing those rows. Best wishes Wolfgang > Hello All, > > > Another problem has come up that hopefully someone can provide some assistance with... > > I am trying to plot ChIP data in relation to the TSS as show in the Starr vignette but the following error comes up when I call the getProfiles function: > >> profile = getProfiles(wtNucRatio, probeAnnot, tssAnno, 800, 800, feature = "TSS", borderNames = "TSS", method = "basewise") > chromosome NA Error in probeAnno[paste(chr[i], "index", sep = ".")] : > No mapping 'NA.index' in this 'probeAnno' object. > > > > > > My particular probeAnno object (probeAnnot) was created using both functions recommended on this board and in the vignette. For example: > > > using the Ringo function of: posToProbeAnno > >> probeAnnot <- posToProbeAnno(pos, genome="Saccer", microarrayPlatform = "Affymetrix") > > or the Starr function of bpmapToProbeAnno > >> probeAnno = bpmapToProbeAnno(bpmap) > > both methods print out the probeAnno mapping for chromosome and do not throw any errors so I assumed the object was made correctly. > > > So I think the error above may be coming from elsewhere but I cannot find it and do not know how to fix it. Any help would be greatly appreciated. > > PS. I created the tssAnno using biomaRt and everything in that looks to be okay... > > noah > > _______________________________________________ > 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 -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact