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  • dpryan
    replied
    You might just try:
    Code:
    rawcounts <- read.delim("counts.txt", header=T, row.names=1)

    Leave a comment:


  • huma Asif
    replied
    can you help me how i can get rid of 1,2,3, in first column
    > head(rawcounts)
    Gene.ID A B
    1 WASH7P 1 0
    2 FAM138A 0 0
    3 FAM138F 0 0
    4 OR4F5 0 0
    5 LOC100132062 0 0
    6 LOC100132287 0 0
    i tried
    rawcounts <- read.delim("counts.txt", header=TRUE, sep="/t", row.names="Gene.ID")
    but it doesnot work

    Leave a comment:


  • huma Asif
    replied
    thank you dpryan

    Leave a comment:


  • dpryan
    replied
    That ID corresponds to whatever you counted on in your annotation file. If the corresponding names are in the file then just load it (see the GenomicFeatures package) and use that. Alternatively, there are annotation packages for many organisms, so just load the appropriate one in R and use it.

    Leave a comment:


  • huma Asif
    replied
    while its going let me explain you a problem about DESeq
    i tried to use input file with genenames but it was giving me this error
    Error in round(countData) : non-numeric argument to mathematical function

    so what i did in analysis i cut the column with gene name
    now problem is the interpretation of result as in output i have id and i am confused how to combine this info with my gene
    i want to attach my count file but here is no option to attach



    output (total)
    id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
    18 32.80688778 4.323701761 61.2900738 14.17537036 3.825314524 0.034361637 0.836923637

    output to see just significant
    id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
    15959 3564.773938 16.43006669 7113.11781 432.9329846 8.757999912 8.02E-20 1.39E-15

    problem here is what this id is telling me and how i am going to combine with gene names

    please do reply atleast this DESeq output will give me an idea to compare with others

    Leave a comment:


  • dpryan
    replied
    Normally you create a character vector containing filenames that you would use (it's usually best to just make a CSV file with all of this and then load it). Otherwise, yes, you have to type it all by hand.

    Leave a comment:


  • huma Asif
    replied
    thank you i read all that but do i need to write names of my count file or path where my files are my current diectory is where my gff and count files are

    Leave a comment:


  • dpryan
    replied
    Please read
    Code:
    help(DEXSeqDataSetFromHTSeq)
    You'll see that the countFiles are the files containing counts produced by dexseq_count.py.

    Leave a comment:


  • huma Asif
    replied
    please help me in creating
    DEXSeqDataSet
    i am confused what shall i give in place of countFiles
    where do i specify my files in this code



    dxd = DEXSeqDataSetFromHTSeq(
    countFiles,
    sampleData=sampleTable,
    design= ˜ sample + exon + condition:exon,
    flattenedfile=flattenedFile )

    Leave a comment:


  • huma Asif
    replied
    > ecs <- read.HTSeqCounts(
    + sampleTable$countFile,
    + sampleTable,
    + flattenedfile="gene.gff")
    Error in checkAtAssignment("character", "annotationFile", "character") :
    ‘annotationFile’ is not a slot in class “character”
    In addition: Warning message:
    'newExonCountSet' is deprecated.
    Use 'DEXSeqDataSet' instead.
    See help("Deprecated")
    Last edited by huma Asif; 08-06-2014, 11:05 AM.

    Leave a comment:


  • huma Asif
    replied
    i am using
    > packageVersion("DEXSeq")
    [1] ‘1.10.8’

    Leave a comment:


  • dpryan
    replied
    What version of DEXseq are you using? That entire method has been deprecated. Anyway, try:
    Code:
    flattenedfile="gene.gff"
    instead of just "gene.gff".

    Leave a comment:


  • huma Asif
    replied
    thanks i downloaded gtf from ucsc

    well i am following instruction in
    Inferring differential exon usage in RNA-Seq data with the DEXSeq package
    done with
    dexseq_prepare_annotation.py script and
    python /path/to/library/DEXSeq/python_scripts/dexseq_count.py
    Dmel_flattenend.gff untreated1.sam untreated1.counts

    done with > sampleTable
    countFile condition libType
    A A.counts control single-end
    B B.counts patient single-end


    need help here
    ecs <- read.HTSeqCounts(
    + sampleTable$countFile,
    + sampleTable,
    + "gene.gff" )

    getting this error
    Error: unexpected string constant in:
    "sampleTable
    "gene.gff""
    Last edited by huma Asif; 08-06-2014, 08:36 AM.

    Leave a comment:


  • dpryan
    replied
    Regarding the Ensembl annotation, you could just use sed or awk to change the chromosome names (note that the mitochondria are chrM in UCSC and MT in Ensembl, so just appending "chr" won't fix everything).

    Regarding the DEXSeq error, it would be helpful to see the command issued and the exact error message.

    Leave a comment:


  • huma Asif
    replied
    for DEXSeq i downloaded Homo_sapiens.gtf from UCSC but it terminate everytime on chr15
    from ensembl it is downloaded successfully but now prob is chr in bam and 1,2,... chromosome notation
    can you guide how to make it compatible

    Leave a comment:

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