Question: Creating Heatmaps with cummeRbund
0
gravatar for rodrigo.nicodemos82
4.0 years ago by
United States
rodrigo.nicodemos8210 wrote:

Hello,

I've been trying to create a heatmap of an RNAseq experiment. I've followed the following online tutorial:

https://wikis.utexas.edu/display/bioiteam/Visualization+using+CummeRbund

However, when I get to creating the heatmap steps:

geneids <- c(up_gene_data$gene_id)
myGenes <- getGenes(cuff_data, geneids)
pdf("Heatmap.pdf")
csHeatmap(myGenes, cluster="both")
dev.off()

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.

Thanks.

Rodrigo

heatmaps rna-seq cummerbund R • 3.6k views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 4.0 years ago by rodrigo.nicodemos8210
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