[BioC] Error using getMeans function in Ringo/Starr

[Noah Dowell]

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         
>