Question: Heatmap with VST Normailzed Data
0
gravatar for pthom010
7 weeks ago by
pthom0100
pthom0100 wrote:

I conducted a time-course with 5 time points and two samples (three replicates for each time point).I have a dds object with 30 columns( one for each replicate) that I have vst-transformed. I have my columns as samples and my rows as transcripts. I have about 8000 DEGs and would like to make a heatmap with all of them to look at genome-wide clusters before I drill down into time-specific samples. I have been using the following function but can't get my heatmap to assemble (R keeps aborting). I assume it is because there are too many DEGs but I was wondering if anybody knew if making the heatmap was feasible.

I have been using the following code (assuming vsd is my vst-transformed dds object with the 8000 DEGs):

heatmap(vsd, Rowv=TRUE, Colv = FALSE, scale = "row")
rna-seq R • 160 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by pthom0100
1
gravatar for Asaf
7 weeks ago by
Asaf8.4k
Israel
Asaf8.4k wrote:

Kevin's tutorial should be useful: https://github.com/kevinblighe/E-MTAB-6141 he uses ComplexHeatmap package, another option is heatmap.2

ADD COMMENTlink written 7 weeks ago by Asaf8.4k

Thank you. I ended up getting to the root of the problem and I can produce the heatmap now. However, I will read these tutorials because ComplexHeatmap looks rather impressive. Thanks!

ADD REPLYlink written 7 weeks ago by pthom0100
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