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  • DEXSeq error - Error in lf[[1]] : subscript out of bounds

    Hi,

    I was going to try DEXSeq for the splicing analysis, but I got stuck at the beginning.
    I got 'subscript out of bounds' errors when tried 'DEXSeqDataSetFromHTSeq'. The error seems to tell me that sample or column numbers were not matching with something else.
    I don't really understand it. Please, somebody tell me what did I do wrong?

    Code:
    library("DEXSeq")
    
    sampleTable <- data.frame(
        rownames = c( "IVF1","IVF2","IVF3",
                      "cSCNT1","cSCNT2","cSCNT3","cSCNT4",
                      "fSCNT1","fSCNT2","fSCNT3","fSCNT4"),
        countFiles = c( "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/IVF1.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/IVF2.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/IVF3.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/cSCNT1.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/cSCNT2.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/cSCNT3.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/cSCNT4.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/fSCNT1.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/fSCNT2.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/fSCNT3.counts",
                       "~/00-NGS/RNAseq/bov/Old_Pico/Ensembl/DEXseq/fSCNT4.counts"),
        condition = c( rep("IVF", 3), rep("cSCNT", 4),rep("fSCNT", 4) ),
        type = c("single","single","single","single","single","single","single","single","single","single","single"))
    sampleTable
    
    flattenedfile="/home/bio1/00-NGS/RNAseq/bov/Old_Pico/Annotation/DEXseq_Bovine_Ensembl.gtf"
    
    dxd = DEXSeqDataSetFromHTSeq(
          countFiles,
          sampleData=sampleTable,
          design= ~ sample + exon + condition:exon,
          flattenedfile=flattenedfile)

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  • seqadmin
    Multiomics Techniques Advancing Disease Research
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    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
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    02-08-2024, 06:33 AM

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