Zhu, Lihua (Julie <julie.zhu at="" ...=""> writes: > > Benedikt, > > I encountered the following error using Starr package to analyze chip-chip data from GeneChip Human > Promoter 1.0R Array > http://www.affymetrix.com/estore/esearch/search.jsp? pd=131461&N=4294967292. Could you please help? > > In addition, there are two bpmap files: Hs_PromPF_v02-3_NCBIv34.bpmap and > Hs_PromPR_v02-3_NCBIv34.bpmap for this array. Is there a way to pass both bpmap files to readBpmap function? > > Many thanks for your help in advance! > > Best regards, > > Julie > > >h3k27R_loess_ratio <- getRatio(h3k27R_loess, ips, controls, description, fkt=median, featureData=F) > Calculating ratio > Building new ExpressionSet > > >peaks <- cmarrt.ma(h3k27R_loess_ratio, probeAnnoR, chr=NULL, M=NULL, frag.length=146) > Error in probeAnno[paste(x, "start", sep = ".")] : > No mapping 'Bs:Jan_2004;NC_000964.start' in this 'probeAnno' object. > Hi Julie, Just wondering if you got an answer to your question or figured it out somehow? I'm getting the exact same error (I'm analyzing medip-chip data) No mapping 'Bs: Jan_2004;NC_000964.start' in this 'probeAnno' object. Thanks! Paul

Paul, I downloaded Bpmap file from cisGenome website,that solved the issue. Best regards, Julie > On Apr 3, 2014, at 5:23 PM, Paul <paul.guilhamon.10 at="" ucl.ac.uk=""> wrote: > > Zhu, Lihua (Julie <julie.zhu at="" ...=""> writes: > >> >> Benedikt, >> >> I encountered the following error using Starr package to analyze chip-chip > data from GeneChip Human >> Promoter 1.0R Array >> http://www.affymetrix.com/estore/esearch/search.jsp? > pd=131461&N=4294967292. Could you please help? >> >> In addition, there are two bpmap files: Hs_PromPF_v02-3_NCBIv34.bpmap and >> Hs_PromPR_v02-3_NCBIv34.bpmap for this array. Is there a way to pass both > bpmap files to readBpmap function? >> >> Many thanks for your help in advance! >> >> Best regards, >> >> Julie >> >>> h3k27R_loess_ratio <- getRatio(h3k27R_loess, ips, controls, description, > fkt=median, featureData=F) >> Calculating ratio >> Building new ExpressionSet >> >>> peaks <- cmarrt.ma(h3k27R_loess_ratio, probeAnnoR, chr=NULL, M=NULL, > frag.length=146) >> Error in probeAnno[paste(x, "start", sep = ".")] : >> No mapping 'Bs:Jan_2004;NC_000964.start' in this 'probeAnno' object. > > > Hi Julie, > Just wondering if you got an answer to your question or figured it out > somehow? I'm getting the exact same error (I'm analyzing medip-chip data) > No mapping 'Bs: Jan_2004;NC_000964.start' in this 'probeAnno' object. > > Thanks! > > Paul > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor