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  • question with read.HTSeqCounts function in DEXSeq package

    Hi,

    recently I tried to use DEXSeq package to estimate the differentially incorporated exons. I had a problem when I am trying to read the files.

    My pipeline is:
    1. annotation_DEXSeq<-"/Users/lxz/Dropbox/protocol/3-database/human_genome/Homo_sapiens.GRCh37.65.DEXSeq.gff"
    2. file_path_ALK<-"/Users/lxz/Dropbox/Lab_Resource/RNAseq/1-data-processing/10-splicing/2-DEXSeq/1-DEXSeq-results"
    3. samples_DHL=data.frame(condition=c(rep("control",3),rep("treated",3)),row.names=dir(file_path_ALK,pattern="DEXSeq_DHL.txt"),stringsAsFactors=TRUE, check.names=FALSE)
    > samples_DHL
    condition
    control01_DEXSeq_DHL.txt control
    control02_DEXSeq_DHL.txt control
    control03_DEXSeq_DHL.txt control
    treated01_DEXSeq_DHL.txt treated
    treated02_DEXSeq_DHL.txt treated
    treated03_DEXSeq_DHL.txt treated

    4. DHL_DEXSeq=read.HTSeqCounts(countfiles=file.path(file_path_ALK,rownames(samples_DHL)),design=samples_DHL,flattenedfile=annotation_DEXSeq)

    the error message is:
    "Error in order(aggregates$gene_id) :
    unimplemented type 'list' in 'orderVector1
    "

    any idea what is the problem and how to fix it?
    Thanks.


    R environment is listed here.
    > sessionInfo()
    R version 2.15.1 (2012-06-22)
    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] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 BiocInstaller_1.8.3

    loaded via a namespace (and not attached):
    [1] biomaRt_2.14.0 hwriter_1.3 RCurl_1.95-3 statmod_1.4.16 stringr_0.6.2 tools_2.15.1
    [7] XML_3.95-0.1

  • #2
    This looks like something is wrong with your flattened annotation file. Have you had a look inside it to check whether it looks alright? Does 'read.HTSeqCounts' work if you don't pass the annotation file?

    Comment


    • #3
      Originally posted by Simon Anders View Post
      This looks like something is wrong with your flattened annotation file. Have you had a look inside it to check whether it looks alright? Does 'read.HTSeqCounts' work if you don't pass the annotation file?
      Hi, Simon:

      thanks. The error message disappear when I did not include the annotation file in the read.HTSeqCounts. I will check whether the downstream analysis work or not.

      I also check the number of the line in reference and output.
      Length of reference is 619124; length of output is 567380.
      So a follow-up question, does this mean if reference and output are not in the same length, then I should not pass annotation file to read.HTSeqCounts?
      Thanks.

      Comment

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