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  • How to build a heatmap using cummerbund with user defined list of genes

    Hi
    I am a newbie learning to use cummerbund for analyzing RNA Seq data.
    I need to build some heatmaps with a list of genes across 2 samples.
    My code is:

    common=c("PLK1","MYBL2","CCND1","CCNB1","E2F1","FOXM1","TOP2A")
    > testcommon=getGenes(cuff1,common)
    >csHeatmap(testcommon,rescaling='none',clustering='none',labCol=F,labRow=T,logMode=T,pseudocount=1.0,border=FALSE,heatscale=c(low='green',mid='black',high='red'),heatMidpoint=NULL)
    The heatmap is attached
    However the order of the genes is random and changes each time my samples change. Could somebody please help me order the genes the way I want?

    Thanks
    Attached Files

  • #2
    Hi
    Did you get answer ?
    You may try using clustering='both'.
    Do you something about error bars in expressionBarplot(mygene), I have very high (big) error bars ??? is it a big error or just can be ignored ?

    Comment


    • #3
      Hi
      do you know, if we can add a dendrogram using csHeatmap ?
      Thank you

      Originally posted by psingh View Post
      Hi
      I am a newbie learning to use cummerbund for analyzing RNA Seq data.
      I need to build some heatmaps with a list of genes across 2 samples.
      My code is:

      common=c("PLK1","MYBL2","CCND1","CCNB1","E2F1","FOXM1","TOP2A")
      > testcommon=getGenes(cuff1,common)
      >csHeatmap(testcommon,rescaling='none',clustering='none',labCol=F,labRow=T,logMode=T,pseudocount=1.0,border=FALSE,heatscale=c(low='green',mid='black',high='red'),heatMidpoint=NULL)
      The heatmap is attached
      However the order of the genes is random and changes each time my samples change. Could somebody please help me order the genes the way I want?

      Thanks

      Comment


      • #4
        Hi psingh,

        Did you manage to find a way to order the genes? Cannot find how to?

        Thanks
        SR

        Comment


        • #5
          I shifted to gplots.
          cummeRbund gives lot scale and without normalization, it is not accepted for publication. I dont know how to normalise using R. Therefore, I mannualy normalized values and created heatmap.

          Originally posted by shleshar View Post
          Hi psingh,

          Did you manage to find a way to order the genes? Cannot find how to?

          Thanks

          Comment

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