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.

>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

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