Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Limma multifactor experiment design matrix

    Hi, so I am very confused as to how I can make a multifactor design for limma RNA differential expression. I've read other posts in different forums and none of the answers are very explicit (to me) as to how to build a multifactor design

    For examples, say I have p1N, p1T, p2N, and p2T, where p# is patient number and N/T is normal tumor.

    I can build a single factor design matrix like this:

    ------Normal------Tumor
    1 ------ 1 --------- 0
    2 ------ 0 --------- 1
    3 ------ 1 --------- 0
    4 ------ 0 --------- 1

    I am completely lost as to how I can build a numeric matrix with multiple factors, which in this case, the factors would be patient number and N/T.

  • #2
    Code:
    d = data.frame(patient=factor(c("p1", "p1", "p2", "p2", ...)),
                   condition=factor(c("N", "T", "N", "T", ...)))
    design = model.matrix(~patient + condition, d)
    N.B., I've likely made a typo somewhere, but that's the gist.

    Comment


    • #3
      Oh, I thought I had to manually build a numeric matrix for the design matrix. Thanks. I have a followup question. I understand that the intercept column that is resulted is used for pair wise comparison. My question is when to use:

      design = model.matrix(~0+patient + condition, d)
      as opposed to this
      design = model.matrix(~patient + condition, d)

      Ok I found this from another post:

      EDIT:
      "This [design = model.matrix(~0+patient + condition, d)] (a cell means model) simply computes the mean expression for each group, and then you have to make all contrasts explicitly. The [design = model.matrix(~patient + condition, d)] has an implicit contrast (everything is a comparison to control), so you have to make contrasts for some comparisons, but not for others."

      from https://support.bioconductor.org/p/57268/


      So is it safe to say this only matters if I am doing a contrast matrix comparison?
      Last edited by Lugalbanda; 10-18-2016, 09:35 AM.

      Comment


      • #4
        Correct, the "0+" is only needed if you want to specify contrasts, which aren't needed to answer your question.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Genetic Variation in Immunogenetics and Antibody Diversity
          by seqadmin



          The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
          11-06-2024, 07:24 PM
        • seqadmin
          Choosing Between NGS and qPCR
          by seqadmin



          Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
          10-18-2024, 07:11 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 11-08-2024, 11:09 AM
        0 responses
        48 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 11-08-2024, 06:13 AM
        0 responses
        32 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 11-01-2024, 06:09 AM
        0 responses
        34 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-30-2024, 05:31 AM
        0 responses
        23 views
        0 likes
        Last Post seqadmin  
        Working...
        X