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  • Problem with ShortRead (R, Bioconductor) function readIntensities

    Hi,

    As I was trying to run Rolexa package for Solexa GAII ChIP-Seq data, I encountered an irresolvable problem already in the initial step: loading the intensity data. I used 'readIntensities' function included in the ShortRead package as follows:

    path = SolexaPath("/data/091029_HWI-EAS419_0050",
    imageAnalysisPath="C1-36_Firecrest1.4.0_02-11-2009_SBSUser")

    int = readIntensities(path, pattern="s_1_0001", withVariability = FALSE)

    ---

    Error: Input/Output
    'readIntensities' failed to parse files
    dirPath: 'C1-36_Firecrest1.4.0_02-11-2009_SBSUser'
    pattern: 's_1_0001'
    type: 'SolexaIntensity'
    error: invalid 'times' argument

    ---

    The path to files is correct, it finds the files:

    s_1_0001_int.txt.p.gz
    s_1_0001_nse.txt.p.gz
    s_1_0001_pos.txt

    It should pick the *int.txt.p.gz file. But something goes wrong. Any suggestions to resolve this are appreciated!

    ---

    > sessionInfo()
    R version 2.10.0 (2009-10-26)
    x86_64-unknown-linux-gnu

    locale:
    [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
    [4] LC_COLLATE=en_US LC_MONETARY=C LC_MESSAGES=en_US
    [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
    [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

    attached base packages:
    [1] stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] Rolexa_1.2.0 ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.0
    [5] Biostrings_2.14.3 IRanges_1.4.4 mclust_3.3.2

    loaded via a namespace (and not attached):
    [1] Biobase_2.6.0 grid_2.10.0 hwriter_1.1



    Kind regards,
    Maria Y.

  • #2
    Hello Maria,

    You should try sending your bug report to the Bioc-sig-sequencing mailing list:


    You'll get help quite fast there from the developers and other advanced users

    Greetings,
    Leo
    L. Collado Torres, Ph.D. student in Biostatistics.

    Comment

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