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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