I've been trying to create a heatmap of an RNAseq experiment. I've followed the following online tutorial:
However, when I get to creating the heatmap steps:
geneids <- c(up_gene_data$gene_id)
myGenes <- getGenes(cuff_data, geneids)
I get this error message:
> csHeatmap(myGenes, cluster="both")
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
and I produce a PDF that is not a proper heatmap. The names of the genes are squished to the right side.
Ive followed suggestions from the following post: Heatmaps from cuffdiff output . However, I am still not getting a proper heatmap.
I also wanted to know if I should also install separately the following packages as recommended in the cummeRbund manual:
RSDLite, ggplot2 v0.9.2, reshape2, plyr, fastcluster, rtracklayer, Gviz and Hmisc.