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  • sindrle
    replied
    No surprise, that worked like a charm!

    Thanks again, Ill try to run DEseq2 now for diff.exp.

    Leave a comment:


  • dpryan
    replied
    Ah, I see what the problem is. colData is is set from SampleTable (it's all but the first 2 columns). However, there's just a single column there and you have two factors in your design. Try the following:

    Code:
    sampleFiles <- list.files(path="/Volumes/timemachine/HTseq_DEseq2",pattern="*.txt")
    status <- factor(c(rep("Healthy",26), rep("Diabetic",22)))
    timepoints = as.factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2))
    sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, status=status, timepoints=timepoints)
    directory <- c("/Volumes/timemachine/HTseq_DEseq2/")
    des <- formula(~timepoints+status)
    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= des)
    Something along those lines should work (I always use DESeqDataSetFromMatrix).

    Leave a comment:


  • sindrle
    replied
    For the first post:

    sampleCondition =read.table("/Volumes/timemachine/HTseq_DEseq2/03_SampleCondition.txt", header=TRUE)
    condition = sampleCondition

    03_SampleCondition.txt:

    Condition
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_pre-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Diabetic_post-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_pre-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Healthy_post-exercise
    Last edited by sindrle; 10-18-2013, 05:57 AM.

    Leave a comment:


  • sindrle
    replied
    Design = des doen not work:

    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= des)
    Error in validObject(.Object) :
    invalid class "DESeqDataSet" object: all variables in design formula must be columns in colData

    Leave a comment:


  • sindrle
    replied
    Heres my "sampleTable":
    sampleName fileName Condition
    1 D104.txt D104.txt Diabetic_pre-exercise
    2 D121.txt D121.txt Diabetic_pre-exercise
    3 D153.txt D153.txt Diabetic_pre-exercise
    4 D155.txt D155.txt Diabetic_pre-exercise
    5 D161.txt D161.txt Diabetic_pre-exercise
    6 D162.txt D162.txt Diabetic_pre-exercise
    7 D167.txt D167.txt Diabetic_pre-exercise
    8 D173.txt D173.txt Diabetic_pre-exercise
    9 D176.txt D176.txt Diabetic_pre-exercise
    10 D177.txt D177.txt Diabetic_pre-exercise
    11 D179.txt D179.txt Diabetic_pre-exercise
    12 D204.txt D204.txt Diabetic_post-exercise
    13 D221.txt D221.txt Diabetic_post-exercise
    14 D253.txt D253.txt Diabetic_post-exercise
    15 D255.txt D255.txt Diabetic_post-exercise
    16 D261.txt D261.txt Diabetic_post-exercise
    17 D262.txt D262.txt Diabetic_post-exercise
    18 D267.txt D267.txt Diabetic_post-exercise
    19 D273.txt D273.txt Diabetic_post-exercise
    20 D276.txt D276.txt Diabetic_post-exercise
    21 D277.txt D277.txt Diabetic_post-exercise
    22 D279.txt D279.txt Diabetic_post-exercise
    23 N101.txt N101.txt Healthy_pre-exercise
    24 N108.txt N108.txt Healthy_pre-exercise
    25 N113.txt N113.txt Healthy_pre-exercise
    26 N170.txt N170.txt Healthy_pre-exercise
    27 N171.txt N171.txt Healthy_pre-exercise
    28 N172.txt N172.txt Healthy_pre-exercise
    29 N175.txt N175.txt Healthy_pre-exercise
    30 N181.txt N181.txt Healthy_pre-exercise
    31 N182.txt N182.txt Healthy_pre-exercise
    32 N183.txt N183.txt Healthy_pre-exercise
    33 N186.txt N186.txt Healthy_pre-exercise
    34 N187.txt N187.txt Healthy_pre-exercise
    35 N188.txt N188.txt Healthy_pre-exercise
    36 N201.txt N201.txt Healthy_post-exercise
    37 N208.txt N208.txt Healthy_post-exercise
    38 N213.txt N213.txt Healthy_post-exercise
    39 N270.txt N270.txt Healthy_post-exercise
    40 N271.txt N271.txt Healthy_post-exercise
    41 N272.txt N272.txt Healthy_post-exercise
    42 N275.txt N275.txt Healthy_post-exercise
    43 N281.txt N281.txt Healthy_post-exercise
    44 N282.txt N282.txt Healthy_post-exercise
    45 N283.txt N283.txt Healthy_post-exercise
    46 N286.txt N286.txt Healthy_post-exercise
    47 N287.txt N287.txt Healthy_post-exercise
    48 N288.txt N288.txt Healthy_post-exercise

    Leave a comment:


  • dpryan
    replied
    What are the dimensions of sampleTable and have you tried "design=des" rather than "design=~des"? For your first post, what were the dimensions of condition?

    Leave a comment:


  • sindrle
    replied
    I have also tried this:

    status <- factor(c(rep("Healthy",26), rep("Diabetic",22)))
    timepoints = c(1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2)
    des <- formula(~timepoints+status)
    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ des)

    Same error..

    Leave a comment:


  • sindrle
    started a topic HTseq-count to DEseq2: Need a little help..

    HTseq-count to DEseq2: Need a little help..

    Hi!
    This is what Ive done:

    sampleFiles <- list.files(path="/Volumes/timemachine/HTseq_DEseq2",pattern="*.txt")
    sampleCondition <- read.table("/Volumes/timemachine/HTseq_DEseq2/03_SampleCondition.txt", header=TRUE)
    sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = sampleCondition)
    directory <- c("/Volumes/timemachine/HTseq_DEseq2/")
    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition)


    Im getting an error:

    "Error in validObject(.Object) :
    invalid class "DESeqDataSet" object: all variables in design formula must be columns in colData"
    Last edited by sindrle; 10-18-2013, 03:56 AM.

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