Benedikt, I encountered the following error using Starr package to analyze chip- chip data from GeneChip Human Promoter 1.0R Array http://www.affymetr ix.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. >h3k27R_loess_ratio ExpressionSet (storageMode: lockedEnvironment) assayData: 4315643 features, 1 samples element names: exprs protocolData: none phenoData sampleNames: H3K27vsIgG varLabels: type varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: >unique(featureData(h3k27F_loess)$chr) [1] AffxCtrl:v1;r2_Tag AffxCtrlBkGrAntiGenomic:v1;gcBin03 AffxCtrlBkGrAntiGenomic:v1;gcBin04 AffxCtrlBkGrAntiGenomic:v1;gcBin05 [5] AffxCtrlBkGrAntiGenomic:v1;gcBin06 AffxCtrlBkGrAntiGenomic:v1;gcBin07 AffxCtrlBkGrAntiGenomic:v1;gcBin08 AffxCtrlBkGrAntiGenomic:v1;gcBin09 [9] AffxCtrlBkGrAntiGenomic:v1;gcBin10 AffxCtrlBkGrAntiGenomic:v1;gcBin11 AffxCtrlBkGrAntiGenomic:v1;gcBin12 AffxCtrlBkGrAntiGenomic:v1;gcBin13 [13] AffxCtrlBkGrAntiGenomic:v1;gcBin14 AffxCtrlBkGrAntiGenomic:v1;gcBin15 AffxCtrlBkGrAntiGenomic:v1;gcBin16 AffxCtrlBkGrAntiGenomic:v1;gcBin17 [17] AffxCtrlBkGrAntiGenomic:v1;gcBin18 AffxCtrlBkGrAntiGenomic:v1;gcBin19 AffxCtrlBkGrAntiGenomic:v1;gcBin20 AffxCtrlBkGrAntiGenomic:v1;gcBin21 [21] AffxCtrlBkGrAntiGenomic:v1;gcBin22 AffxCtrlBkGrAntiGenomic:v1;gcBin23 AffxCtrlBkGrAntiGenomic:v1;gcBin24 AffxCtrlBkGrAntiGenomic:v1;gcBin25 [25] AffxCtrlBkGrGenomic:v1;gcBin04 AffxCtrlBkGrGenomic:v1;gcBin05 AffxCtrlBkGrGenomic:v1;gcBin06 AffxCtrlBkGrGenomic:v1;gcBin07 [29] AffxCtrlBkGrGenomic:v1;gcBin08 AffxCtrlBkGrGenomic:v1;gcBin09 AffxCtrlBkGrGenomic:v1;gcBin10 AffxCtrlBkGrGenomic:v1;gcBin11 [33] AffxCtrlBkGrGenomic:v1;gcBin12 AffxCtrlBkGrGenomic:v1;gcBin13 AffxCtrlBkGrGenomic:v1;gcBin14 AffxCtrlBkGrGenomic:v1;gcBin15 [37] AffxCtrlBkGrGenomic:v1;gcBin16 AffxCtrlBkGrGenomic:v1;gcBin17 AffxCtrlBkGrGenomic:v1;gcBin18 AffxCtrlBkGrGenomic:v1;gcBin19 [41] AffxCtrlBkGrGenomic:v1;gcBin20 AffxCtrlBkGrGenomic:v1;gcBin21 AffxCtrlBkGrGenomic:v1;gcBin22 AffxCtrlBkGrGenomic:v1;gcBin23 [45] AffxCtrlBs:v1;r2_dap AffxCtrlBs:v1;r2_lys AffxCtrlBs:v1;r2_phe AffxCtrlBs:v1;r2_thr [49] AffxCtrlEc:v1;r2_bioB AffxCtrlEc:v1;r2_bioC AffxCtrlEc:v1;r2_bioD AffxCtrlP1:v1;r2_cre [53] At:TIGRv5;chloroplast At:TIGRv5;chr1 At:TIGRv5;chr2 At:TIGRv5;chr3 [57] At:TIGRv5;chr4 At:TIGRv5;chr5 Bs:Jan_2004;NC_000964.1 Hs:NCBIv34;chr1 [61] Hs:NCBIv34;chr10 Hs:NCBIv34;chr11 Hs:NCBIv34;chr12 Hs:NCBIv34;chr13 [65] Hs:NCBIv34;chr14 Hs:NCBIv34;chr15 Hs:NCBIv34;chr16 Hs:NCBIv34;chr17 [69] Hs:NCBIv34;chr18 Hs:NCBIv34;chr19 Hs:NCBIv34;chr2 Hs:NCBIv34;chr20 [73] Hs:NCBIv34;chr21 Hs:NCBIv34;chr22 Hs:NCBIv34;chr3 Hs:NCBIv34;chr4 [77] Hs:NCBIv34;chr5 Hs:NCBIv34;chr6 Hs:NCBIv34;chr7 Hs:NCBIv34;chr8 [81] Hs:NCBIv34;chr9 Hs:NCBIv34;chrM Hs:NCBIv34;chrX Hs:NCBIv34;chrY >probeAnnoR A 'probeAnno' object holding the mapping between reporters and genomic positions. Chromosomes: AffxCtrl:v1;r2_Tag AffxCtrlBkGrAntiGenomic:v1;gcBin03 AffxCtrlBkGrAntiGenomic:v1;gcBin04 AffxCtrlBkGrAntiGenomic:v1;gcBin05 AffxCtrlBkGrAntiGenomic:v1;gcBin06 AffxCtrlBkGrAntiGenomic:v1;gcBin07 AffxCtrlBkGrAntiGenomic:v1;gcBin08 AffxCtrlBkGrAntiGenomic:v1;gcBin09 AffxCtrlBkGrAntiGenomic:v1;gcBin10 AffxCtrlBkGrAntiGenomic:v1;gcBin11 AffxCtrlBkGrAntiGenomic:v1;gcBin12 AffxCtrlBkGrAntiGenomic:v1;gcBin13 AffxCtrlBkGrAntiGenomic:v1;gcBin14 AffxCtrlBkGrAntiGenomic:v1;gcBin15 AffxCtrlBkGrAntiGenomic:v1;gcBin16 AffxCtrlBkGrAntiGenomic:v1;gcBin17 AffxCtrlBkGrAntiGenomic:v1;gcBin18 AffxCtrlBkGrAntiGenomic:v1;gcBin19 AffxCtrlBkGrAntiGenomic:v1;gcBin20 AffxCtrlBkGrAntiGenomic:v1;gcBin21 AffxCtrlBkGrAntiGenomic:v1;gcBin22 AffxCtrlBkGrAntiGenomic:v1;gcBin23 AffxCtrlBkGrAntiGenomic:v1;gcBin24 AffxCtrlBkGrAntiGenomic:v1;gcBin25 AffxCtrlBkGrGenomic:v1;gcBin04 AffxCtrlBkGrGenomic:v1;gcBin05 AffxCtrlBkGrGenomic:v1;gcBin06 AffxCtrlBkGrGenomic:v1;gcBin07 AffxCtrlBkGrGenomic:v1;gcBin08 AffxCtrlBkGrGenomic:v1;gcBin09 AffxCtrlBkGrGenomic:v1;gcBin10 AffxCtrlBkGrGenomic:v1;gcBin11 AffxCtrlBkGrGenomic:v1;gcBin12 AffxCtrlBkGrGenomic:v1;gcBin13 AffxCtrlBkGrGenomic:v1;gcBin14 AffxCtrlBkGrGenomic:v1;gcBin15 AffxCtrlBkGrGenomic:v1;gcBin16 AffxCtrlBkGrGenomic:v1;gcBin17 AffxCtrlBkGrGenomic:v1;gcBin18 AffxCtrlBkGrGenomic:v1;gcBin19 AffxCtrlBkGrGenomic:v1;gcBin20 AffxCtrlBkGrGenomic:v1;gcBin21 AffxCtrlBkGrGenomic:v1;gcBin22 AffxCtrlBkGrGenomic:v1;gcBin23 AffxCtrlBs:v1;r2_dap AffxCtrlBs:v1;r2_lys AffxCtrlBs:v1;r2_phe AffxCtrlBs:v1;r2_thr AffxCtrlEc:v1;r2_bioB AffxCtrlEc:v1;r2_bioC AffxCtrlEc:v1;r2_bioD AffxCtrlP1:v1;r2_cre At:TIGRv5;chloroplast At:TIGRv5;chr1 At:TIGRv5;chr2 At:TIGRv5;chr3 At:TIGRv5;chr4 At:TIGRv5;chr5 Bs:Jan_2004;NC_000964.1 Hs:NCBIv34;chr1 Hs:NCBIv34;chr10 Hs:NCBIv34;chr11 Hs:NCBIv34;chr12 Hs:NCBIv34;chr13 Hs:NCBIv34;chr14 Hs:NCBIv34;chr15 Hs:NCBIv34;chr16 Hs:NCBIv34;chr17 Hs:NCBIv34;chr18 Hs:NCBIv34;chr19 Hs:NCBIv34;chr2 Hs:NCBIv34;chr20 Hs:NCBIv34;chr21 Hs:NCBIv34;chr22 Hs:NCBIv34;chr3 Hs:NCBIv34;chr4 Hs:NCBIv34;chr5 Hs:NCBIv34;chr6 Hs:NCBIv34;chr7 Hs:NCBIv34;chr8 Hs:NCBIv34;chr9 Hs:NCBIv34;chrM Hs:NCBIv34;chrX Hs:NCBIv34;chrY sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] Starr_1.18.1 affxparser_1.34.2 affy_1.40.0 Ringo_1.26.1 lattice_0.20-27 Matrix_1.1-2-2 limma_3.18.13 [8] RColorBrewer_1.0-5 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 annotate_1.40.1 AnnotationDbi_1.24.0 BiocInstaller_1.12.0 DBI_0.2-7 genefilter_1.44.0 [7] IRanges_1.20.7 MASS_7.3-30 preprocessCore_1.24.0 pspline_1.0-16 RSQLite_0.11.4 splines_3.0.2 [13] stats4_3.0.2 survival_2.37-7 tools_3.0.2 vsn_3.30.0 XML_3.95-0.2 xtable_1.7-3 [19] zlibbioc_1.8.0 [[alternative HTML version deleted]]