[BioC] Error using getMeans function in Ringo/Starr

[Noah Dowell]

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         
>> > 
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> 
>