[BioC] Error using getMeans function in Ringo/Starr

[zacher at lmb.uni-muenchen.de]

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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