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  • #16
    i am using
    > packageVersion("DEXSeq")
    [1] ‘1.10.8’

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    • #17
      > 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.

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      • #18
        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 )

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        • #19
          Please read
          Code:
          help(DEXSeqDataSetFromHTSeq)
          You'll see that the countFiles are the files containing counts produced by dexseq_count.py.

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          • #20
            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

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            • #21
              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.

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              • #22
                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

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                • #23
                  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.

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                  • #24
                    thank you dpryan

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                    • #25
                      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

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                      • #26
                        You might just try:
                        Code:
                        rawcounts <- read.delim("counts.txt", header=T, row.names=1)

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