Entering edit mode
Noah Dowell
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410
@noah-dowell-3791
Last seen 10.2 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
>
