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  • goseq error message

    I’m a molecular biologist trying to teach myself some bioinformatics. At the moment, I’m using the goseq package to analyse differentially expressed genes in my rnaseq data set. I’m using the function nullp to calculate a probability weighting function. As my genome/geneID is not supported by goseq, I have calculated the gene lengths manually using:

    txsByGene=transcriptsBy(txdb,"gene")
    lengthData=median(width(txsByGene))

    I then input the lengthData vector into:

    pwf=nullp(genes,’bosTau6’,ensGene’,bias.data=lengthData)

    Error in nullp(genes, "bosTau6", "ensGene", "lengthData") :
    bias.data vector must have the same length as DEgenes vector!

    I check the lengths of the ‘genes’ and ‘lengthData’ vectors and they are the same i.e 24616. Any ideas why R is reporting that the 2 vectors have different lengths?

    lengthData vector:

    ENSBTAG00000000005 ENSBTAG00000000008 ENSBTAG00000000009
    89702.0 30289.0 2973.0

    ….

    genes vector:

    ENSBTAG00000000005 ENSBTAG00000000008 ENSBTAG00000000009
    0 0 0

    ….

    Thanks

  • #2
    hello All!
    I am desperately trying to run this GO analysis on my RNAseq data(human samples).
    I got stuck in creating a pwf file: I have -I guess- successfully created a DE matrix, with ENS id and 0/1 as identifier of diff-non diff expressed genes.
    here is the error message I encounter
    genes
    0 1
    19004 6715
    > pwf <- nullp(genes, "hg19", "ensGene")
    Loading hg19 length data...
    Error in qr.R(qrx) :
    could not find symbol "..." in environment of the generic function
    I noticed that the ENS ids in my matrix are not into double quotes...I am not sure if it really has an effect...I have just followed the manual step by step, but I am not able to figure out why is not going through (and I am newbie in all this).
    Anybody can help?!!

    Manu
    > sessionInfo()
    R version 2.15.2 (2012-10-26)
    Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

    other attached packages:
    [1] goseq_1.10.0 geneLenDataBase_0.99.10 BiasedUrn_1.05 edgeR_3.0.8 limma_3.14.4 BiocInstaller_1.8.3

    loaded via a namespace (and not attached):
    [1] AnnotationDbi_1.20.7 Biobase_2.18.0 BiocGenerics_0.4.0 biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-4.2 BSgenome_1.26.1
    [8] DBI_0.2-5 GenomicFeatures_1.10.2 GenomicRanges_1.10.7 grid_2.15.2 IRanges_1.16.6 lattice_0.20-15 Matrix_1.0-12
    [15] mgcv_1.7-22 nlme_3.1-108 parallel_2.15.2 RCurl_1.95-4.1 Rsamtools_1.10.2 RSQLite_0.11.2 rtracklayer_1.18.2
    [22] stats4_2.15.2 tools_2.15.2 XML_3.96-1.1 zlibbioc_1.4.0

    Comment

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