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  • msSigPro packages error in edesign

    Dear all,

    I am trying to use maSigPro packages for my next generation counts data. If someone have expression pls help me.
    I have one experimental condition with replicates and their corresponding times (4 time point).
    my script is as follows:
    wt <- read.table("glmNB_wt_r.txt", header=T)
    wt.edesign <- read.table("edesign_wt_r.txt", header=T)
    d <- make.design.matrix (wt.edesign, degree=4) ### i guess i have 4 times thats why degree should be 4
    head (d)

    > head (d)
    $dis
    Time Time2 Time3 Time4
    WT.T1.1 1 1 1 1
    WT.T1.2 1 1 1 1
    WT.T1.3 1 1 1 1
    WT.T2.1 12 144 1728 20736
    ...........
    ............
    WT.T4.6 36 1296 46656 1679616

    $groups.vector
    [1] "Group" "Group" "Group" "Group"

    $edesign
    Time Replicates Group
    WT.T1.1 1 1 1
    WT.T1.2 1 1 1
    WT.T1.3 1 1 1
    WT.T2.1 12 2 1
    WT.T2.2 12 2 1
    WT.T2.3 12 2 1
    WT.T2.4 12 2 1
    WT.T3.1 21 3 1
    WT.T3.2 21 3 1
    WT.T3.3 21 3 1
    WT.T3.4 21 3 1
    WT.T4.1 36 4 1
    WT.T4.2 36 4 1
    WT.T4.3 36 4 1
    WT.T4.4 36 4 1
    WT.T4.5 36 4 1
    WT.T4.6 36 4 1

    library(MASS)
    > NBp <- p.vector (wt, d, counts =T)
    [1] "fitting gene 100 out of 1194"
    [1] "fitting gene 200 out of 1194"
    .......
    [1] "fitting gene 1100 out of 1194"
    > NBt <- T.fit(NBp)
    [1] "fitting gene 100 out of 384"
    [1] "fitting gene 200 out of 384"
    [1] "fitting gene 300 out of 384" ### end

    > get <- get.siggenes(NBt, vars= "each")
    > get$summary
    independ Time Time2 Time3
    1 mmu-miR-106b-5p mmu-miR-106b-5p mmu-miR-106b-5p mmu-miR-106b-5p
    ......
    ....

    Time4
    1 mmu-miR-206-3p
    2 mmu-miR-490-3p
    3 ....... ###blank lines

    > see.genes(get$sig.genes)
    Error in 3:ncol(edesign) : argument of length 0 ?????

    What is the problem here ?? help me please.

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