Hi
I have 4 data files generated from 2 lanes of a Solexa paired-end run.
The qa function worked fine, but the readAligned gave me an error:
>qaSummary = qa("/../data", type="SolexaExport")
> qaSummary
class: SolexaExportQA(9)
QA elements (access with qa[["elt"]]):
readCounts: data.frame(4 3)
baseCalls: data.frame(4 5)
readQualityScore: data.frame(6144 4)
baseQuality: data.frame(376 3)
alignQuality: data.frame(279 3)
frequentSequences: data.frame(600 4)
sequenceDistribution: data.frame(4928 4)
perCycle: list(2)
baseCall: data.frame(800 4)
quality: data.frame(3830 5)
perTile: list(2)
readCounts: data.frame(1200 4)
medianReadQualityScore: data.frame(1200 4)
> qaSummary[["readCounts"]]
read filtered aligned
s_2_1_export.txt 12915438 7665822 7080343
s_2_2_export.txt 12915438 7665822 7277877
s_3_1_export.txt 17296866 7452595 7892453
s_3_2_export.txt 17296866 7452595 8086091
>
When I tried to read all 4 files, I got the error below:
>aln = readAligned("/../data", type="SolexaExport")
Error: Input/Output
'readAligned' failed to parse files
dirPath: '/../data'
pattern: ''
type: 'SolexaExport'
error: negative length vectors are not allowed
>
> sessioInfo()
R version 2.8.1 Patched (2009-03-03 r48046)
i386-apple-darwin9.6.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ShortRead_1.0.6 lattice_0.17-20 Biobase_2.2.2 Biostrings_2.10.16
[5] IRanges_1.0.13
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