Starr package: cmarrt.ma error
0
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
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]]
Starr Starr • 650 views
ADD COMMENT

Login before adding your answer.

Traffic: 368 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6