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  • cummeRbund partitioning and heatmap

    Hi guys,

    I'm playing around with cummeRbund, and I have some questions I would like to ask you.

    First, I would like to cluster a subset of genes and to plot them in a heatmap. I found on this forum how to create a list of genes, and how to draw a heatmap.

    > myIDs<-read.table("text.txt")
    > myIDs<-as.vector(myIDs$V1)
    > myGenes<-getGenes(cuff,myIDs)

    > h<-csHeatmap(myGenes,cluster='both')
    > h



    Now that gives a heatmap with the genes I want, but I somehow think that the clustering is not adequate. I tried to do the partitioning thing like so :

    > ic<-csCluster(myGenes,k=4)

    And then, I figured I could only draw a heatmap with the output of csCluster

    > hic<-csHeatmap(ic)

    And of course it doesn't work.

    Do you guys know how I could plot a heatmap from the csCluster?

    Thanks!

  • #2
    did you get the answer?



    Originally posted by Galgarad View Post
    Hi guys,

    I'm playing around with cummeRbund, and I have some questions I would like to ask you.

    First, I would like to cluster a subset of genes and to plot them in a heatmap. I found on this forum how to create a list of genes, and how to draw a heatmap.

    > myIDs<-read.table("text.txt")
    > myIDs<-as.vector(myIDs$V1)
    > myGenes<-getGenes(cuff,myIDs)

    > h<-csHeatmap(myGenes,cluster='both')
    > h



    Now that gives a heatmap with the genes I want, but I somehow think that the clustering is not adequate. I tried to do the partitioning thing like so :

    > ic<-csCluster(myGenes,k=4)

    And then, I figured I could only draw a heatmap with the output of csCluster

    > hic<-csHeatmap(ic)

    And of course it doesn't work.

    Do you guys know how I could plot a heatmap from the csCluster?

    Thanks!

    Comment


    • #3
      No, I didn't.

      However, I figured a way to do it in R, without cummeRbund. It is not elegant, but it works well! Let me know if you want to see it.

      Comment


      • #4
        Please tell me how you have managed to do. I need to make heatmap with -1 0 +1 range (not the log 10 RPKM value).
        Can you reply please.
        Thank you


        Originally posted by Galgarad View Post
        No, I didn't.

        However, I figured a way to do it in R, without cummeRbund. It is not elegant, but it works well! Let me know if you want to see it.

        Comment


        • #5
          I will.

          Are you familiar with R?

          Comment


          • #6
            Yes, I am using cummeRbund.

            Comment


            • #7
              Hello everybody,

              I ran the cuffdiff analysis on 8 samples and I ran the csCluster command in cummeRbund in order to clusterize genes in my samples.
              I would like to clusterize genes considering only a subset of my samples (ex. only four samples). Is there the possibility to select the samples for which I want to clusterize the genes?
              thanks

              Comment

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