Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • unique379
    Member
    • Aug 2012
    • 27

    #1

    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.

Latest Articles

Collapse

  • SEQadmin2
    16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by SEQadmin2




    NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
    10-30-2026, 06:46 AM
  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
36 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-28-2026, 09:51 AM
0 responses
22 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 11:13 AM
0 responses
72 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 10:48 AM
0 responses
48 views
0 reactions
Last Post SEQadmin2  
Working...