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  • #16
    My experiment is complicated (at least in my mind =) ). I have three time points (0,24,48 hrs) and two conditions (siControl and siTarget) for a total of 6 groups. I'm trying to see how knockdown of my target affects the transcriptome at each time point.

    This information is the closest I can find online that describes how to make a log2-fold change heat map and a dendrogram.... but I'm having some troubles. Can anyone please help?

    A few questions so far:

    1. sigGenes <- getSig(cuff,'BY4741','ino80',alpha=0.05,level='genes')
    -Why were only two of your groups selected here and not the whole data set? Does this impact the final result?

    2. db <- logFC(db,mutants=mut,WT=WT,logBase=2,pseudo=1)
    -when i enter this, I get an error message: Error in db[, mutants] : incorrect number of dimensions

    Comment


    • #17
      Sorry clicked too fast...

      Sorry I should add that so far I have done this:
      >WT<-"C1"
      > mut<-c("C2","C3","C4","C5","C6")

      Originally posted by gareth.lim View Post
      My experiment is complicated (at least in my mind =) ). I have three time points (0,24,48 hrs) and two conditions (siControl and siTarget) for a total of 6 groups. I'm trying to see how knockdown of my target affects the transcriptome at each time point.

      This information is the closest I can find online that describes how to make a log2-fold change heat map and a dendrogram.... but I'm having some troubles. Can anyone please help?

      A few questions so far:

      1. sigGenes <- getSig(cuff,'BY4741','ino80',alpha=0.05,level='genes')
      -Why were only two of your groups selected here and not the whole data set? Does this impact the final result?

      2. db <- logFC(db,mutants=mut,WT=WT,logBase=2,pseudo=1)
      -when i enter this, I get an error message: Error in db[, mutants] : incorrect number of dimensions

      Comment

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