Error using getMeans function in Ringo/Starr
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Noah Dowell ▴ 410
@noah-dowell-3791
Last seen 8.1 years ago
Hello All, I am having some problems with the getMeans function in the Ringo and Starr packages not working in my hands with my data set. I couldn't find references to this error (see below) in the list archive. I have been able to get nearly every other function in these packages to work on my expressionSet without any problems. My probeAnno object was built with the bpmapToProbeAnno function and worked fine for other functions like the computeRunningMedians or the findChersOnSmoothed. I am using the Affymetrix Yeast Tiling Arrays. Thank you for any input. Noah ##Here is the error: > meanData <- getMeans(wtDataRatio, probeAnno, transcriptAnno2[which(transcriptAnno2$name %in% filteredIDs), ], info) Mapping annotated features to spotted probes Error in probeAnno[paste(chr[i], "end", sep = ".")] : No mapping 'NA.end' in this 'probeAnno' object. In addition: Warning messages: 1: In max(i) : no non-missing arguments to max; returning -Inf 2: In max(i) : no non-missing arguments to max; returning -Inf ## When I print out the expressionSet I see in the phenoData there is type "NA" and I wonder if this is the source of the error. > wtDataRatio ExpressionSet (storageMode: lockedEnvironment) assayData: 2697594 features, 1 samples element names: exprs protocolData: none phenoData sampleNames: WTdatavsInput varLabels and varMetadata description: type: NA featureData featureNames: 1, 2, ..., 2697594 (2697594 total) fvarLabels and fvarMetadata description: chr: Chromosome seq: Probe sequence pos: Probe start experimentData: use 'experimentData(object)' Annotation: ## Looking to see how many "NA.end" things there are with the following: > table(wtDataRatio$type == "NA.end") FALSE 1 > sessionInfo() R version 2.11.0 (2010-04-22) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.8.1 RCurl_1.3-1 bitops_1.0-4.1 IRanges_1.6.0 Starr_1.4.0 [6] affxparser_1.20.0 affy_1.26.0 Ringo_1.12.0 Matrix_0.999375-38 lattice_0.18-5 [11] limma_3.4.0 RColorBrewer_1.0-2 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.0 AnnotationDbi_1.10.0 Biostrings_2.16.0 [5] BSgenome_1.16.0 DBI_0.2-5 genefilter_1.30.0 GenomicRanges_1.0.1 [9] MASS_7.3-5 preprocessCore_1.10.0 pspline_1.0-14 RSQLite_0.8-4 [13] splines_2.11.0 survival_2.35-8 tools_2.11.0 XML_2.8-1 [17] xtable_1.5-6 >
Yeast probe Ringo Yeast probe Ringo • 944 views
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@zacherlmbuni-muenchende-3726
Last seen 8.1 years ago
Dear Noah, do the annotation and the probeAnno object use the same name for the chromosomes? Regards, Benedikt Noah Dowell <noahd at="" ucla.edu=""> schrieb : > Hello All, > > I am having some problems with the getMeans function in the Ringo and Starr > packages not working in my hands with my data set. I couldn't find references > to this error (see below) in the list archive. I have been able to get nearly > every other function in these packages to work on my expressionSet without any > problems. My probeAnno object was built with the bpmapToProbeAnno function and > worked fine for other functions like the computeRunningMedians or the > findChersOnSmoothed. I am using the Affymetrix Yeast Tiling Arrays. Thank you > for any input. > > Noah > > > > > > ##Here is the error: > > > meanData <- getMeans(wtDataRatio, probeAnno, > transcriptAnno2[which(transcriptAnno2$name %in% filteredIDs), ], info) > Mapping annotated features to spotted probes > Error in probeAnno[paste(chr[i], "end", sep = ".")] : > No mapping 'NA.end' in this 'probeAnno' object. > In addition: Warning messages: > 1: In max(i) : no non-missing arguments to max; returning -Inf > 2: In max(i) : no non-missing arguments to max; returning -Inf > > ## When I print out the expressionSet I see in the phenoData there is type > "NA" and I wonder if this is the source of the error. > > > > wtDataRatio > ExpressionSet (storageMode: lockedEnvironment) > assayData: 2697594 features, 1 samples > element names: exprs > protocolData: none > phenoData > sampleNames: WTdatavsInput > varLabels and varMetadata description: > type: NA > featureData > featureNames: 1, 2, ..., 2697594 (2697594 total) > fvarLabels and fvarMetadata description: > chr: Chromosome > seq: Probe sequence > pos: Probe start > experimentData: use 'experimentData(object)' > Annotation: > > ## Looking to see how many "NA.end" things there are with the > following: > > > table(wtDataRatio$type == "NA.end") > > FALSE > 1 > > > > > > > > sessionInfo() > R version 2.11.0 (2010-04-22) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] rtracklayer_1.8.1 RCurl_1.3-1 bitops_1.0-4.1 IRanges_1.6.0 > Starr_1.4.0 > [6] affxparser_1.20.0 affy_1.26.0 Ringo_1.12.0 > Matrix_0.999375-38 lattice_0.18-5 > [11] limma_3.4.0 RColorBrewer_1.0-2 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.0 AnnotationDbi_1.10.0 > Biostrings_2.16.0 > [5] BSgenome_1.16.0 DBI_0.2-5 genefilter_1.30.0 > GenomicRanges_1.0.1 > [9] MASS_7.3-5 preprocessCore_1.10.0 pspline_1.0-14 > RSQLite_0.8-4 > [13] splines_2.11.0 survival_2.35-8 tools_2.11.0 > XML_2.8-1 > [17] xtable_1.5-6 > > > _______________________________________________ > 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
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Dear Benedikt, Thanks for the reply. Yes, the annotation file (transcriptAnno in my case) and probeAnno refer to the chromosomes by the same name. Although, this appears to be a different format than what is used by the Nimblegen arrays and the Ringo vignette. I included the printout of the names below for anyone else following along. Best, noah > head(transcriptAnno) chr start end strand name 1 Sc:Oct_2003;chr1 335 649 1 YAL069W 2 Sc:Oct_2003;chr1 80711 81952 -1 YAL034C 3 Sc:Oct_2003;chr1 538 792 1 YAL068W-A 4 Sc:Oct_2003;chr1 101566 105873 -1 YAL024C 5 Sc:Oct_2003;chr1 113615 114616 -1 YAL020C 6 Sc:Oct_2003;chr1 224554 224853 -1 YAR070C > probeAnno 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 AffxCtrlBs:v1;X_Dap AffxCtrlBs:v1;X_Lys AffxCtrlBs:v1;X_Phe AffxCtrlBs:v1;X_Thr AffxCtrlBs:v1;X_Trpn AffxCtrlEc:v1;r2_bioB AffxCtrlEc:v1;r2_bioC AffxCtrlEc:v1;r2_bioD AffxCtrlHouseKeepingSc:v1;18sr AffxCtrlHouseKeepingSc:v1;25sr AffxCtrlHouseKeepingSc:v1;YER022w AffxCtrlHouseKeepingSc:v1;YER148w AffxCtrlHouseKeepingSc:v1;YFL039C 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 Sc:Oct_2003;chr1 Sc:Oct_2003;chr10 Sc:Oct_2003;chr11 Sc:Oct_2003;chr12 Sc:Oct_2003;chr13 Sc:Oct_2003;chr14 Sc:Oct_2003;chr15 Sc:Oct_2003;chr16 Sc:Oct_2003;chr2 Sc:Oct_2003;chr3 Sc:Oct_2003;chr4 Sc:Oct_2003;chr5 Sc:Oct_2003;chr6 Sc:Oct_2003;chr7 Sc:Oct_2003;chr8 Sc:Oct_2003;chr9 Sc:Oct_2003;mitochondrion Sc:Oct_2003;plasmid Microarray platform: Genome: On May 7, 2010, at 3:00 AM, <zacher at="" lmb.uni-muenchen.de=""> <zacher at="" lmb.uni-muenchen.de=""> wrote: > > Dear Noah, > > do the annotation and the probeAnno object use the same name for the chromosomes? > Regards, > > Benedikt > > Noah Dowell <noahd at="" ucla.edu=""> schrieb : > >> Hello All, >> >> I am having some problems with the getMeans function in the Ringo and Starr >> packages not working in my hands with my data set. I couldn't find references >> to this error (see below) in the list archive. I have been able to get nearly >> every other function in these packages to work on my expressionSet without any >> problems. My probeAnno object was built with the bpmapToProbeAnno function and >> worked fine for other functions like the computeRunningMedians or the >> findChersOnSmoothed. I am using the Affymetrix Yeast Tiling Arrays. Thank you >> for any input. >> >> Noah >> >> >> >> >> >> ##Here is the error: >> >> > meanData <- getMeans(wtDataRatio, probeAnno, >> transcriptAnno2[which(transcriptAnno2$name %in% filteredIDs), ], info) >> Mapping annotated features to spotted probes >> Error in probeAnno[paste(chr[i], "end", sep = ".")] : >> No mapping 'NA.end' in this 'probeAnno' object. >> In addition: Warning messages: >> 1: In max(i) : no non-missing arguments to max; returning -Inf >> 2: In max(i) : no non-missing arguments to max; returning -Inf >> >> ## When I print out the expressionSet I see in the phenoData there is type >> "NA" and I wonder if this is the source of the error. >> >> >> > wtDataRatio >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 2697594 features, 1 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: WTdatavsInput >> varLabels and varMetadata description: >> type: NA >> featureData >> featureNames: 1, 2, ..., 2697594 (2697594 total) >> fvarLabels and fvarMetadata description: >> chr: Chromosome >> seq: Probe sequence >> pos: Probe start >> experimentData: use 'experimentData(object)' >> Annotation: >> >> ## Looking to see how many "NA.end" things there are with the >> following: >> >> > table(wtDataRatio$type == "NA.end") >> >> FALSE >> 1 >> >> >> >> >> >> >> > sessionInfo() >> R version 2.11.0 (2010-04-22) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods base >> >> >> other attached packages: >> [1] rtracklayer_1.8.1 RCurl_1.3-1 bitops_1.0-4.1 IRanges_1.6.0 >> Starr_1.4.0 >> [6] affxparser_1.20.0 affy_1.26.0 Ringo_1.12.0 >> Matrix_0.999375-38 lattice_0.18-5 >> [11] limma_3.4.0 RColorBrewer_1.0-2 Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.16.0 annotate_1.26.0 AnnotationDbi_1.10.0 >> Biostrings_2.16.0 >> [5] BSgenome_1.16.0 DBI_0.2-5 genefilter_1.30.0 >> GenomicRanges_1.0.1 >> [9] MASS_7.3-5 preprocessCore_1.10.0 pspline_1.0-14 >> RSQLite_0.8-4 >> [13] splines_2.11.0 survival_2.35-8 tools_2.11.0 >> XML_2.8-1 >> [17] xtable_1.5-6 >> > >> _______________________________________________ >> 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 > >
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Noah Dowell ▴ 410
@noah-dowell-3791
Last seen 8.1 years ago
Dear Benedikt, Converting to class "character" fixed the error. The plot looks great. Thank you for your help and for developing this excellent package! Best, Noah (I am posting to the list in case anyone is following along and can piece together that past couple emails.) On May 10, 2010, at 2:00 AM, <zacher at="" lmb.uni-muenchen.de=""> <zacher at="" lmb.uni-muenchen.de=""> wrote: > > Dear Noah, > > I think the problem could be that the chr and the name column are of class factor: > >> class(transcriptAnno$chr) > [1] "factor" >> class(transcriptAnno$name) > [1] "factor" > > Please convert it to class "character": > >> transcriptAnno$chr = as.character(transcriptAnno$chr) >> class(transcriptAnno$chr) > [1] "character" > > Please tell me if it works, that I can include a check into the function. > Regards, > > Benedikt > > > Noah Dowell <noahd at="" ucla.edu=""> schrieb : > >> Dear Benedikt, >> >> Thank you for looking into this for me. I have attached the transcriptAnno >> object I am using as a RData file. I created this file originally using bioMart >> and it works with the getProfiles function in Ringo/Starr. >> >> Best, >> >> Noah > >
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