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  • Generating heat maps with CummeRbund

    Hi all! I am trying to generate heat maps between two treatments (n=3, each). I would like to do the following:

    Generate a heat map with each individual sample present.
    Generate a heat map with the average expression among samples within the same treatment.

    I am able to generate these two heat maps, but am having two problems:
    1) I would like to take out the ENS# from the heat map and just show the gene name.
    2) When these two heat maps are generated, using the following codes:

    csHeatmap(sig_genes,cluster='both')
    csHeatmap(sig_genes,cluster='both',replicates=T)

    , the order of the genes shown is different. Is there any way to have them in the same order, so that I can line them up next to one another in a graph?

    Thanks in advance for replies!

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