Question: Making a Group Tree using RNA-seq Read Count in R
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gravatar for minuate126
9 weeks ago by
minuate1260
minuate1260 wrote:

Hi. I'm struggling with making group tree. The data format looks like this:

# Genes    Group A .  Group B .  Group C .  Group D
# gene A      15        20         30         20 
# gene B      0         3          20         10 
# gene C      1         7          40         20
# ...

So I want to use hierarchical clustering method to divide those group. Is there any packages or any method to do this in R?

rna-seq tool R • 139 views
ADD COMMENTlink modified 9 weeks ago by Biogeek350 • written 9 weeks ago by minuate1260
0
gravatar for Biogeek
9 weeks ago by
Biogeek350
Biogeek350 wrote:

Hi Minuate,

Can you please specify what sort of 'tree'? Do you mean a heatmap or dendrogram based figure? If so you can use heatmap.2 or pheatmap in R. In conjunction with ggplots2 and other various R modules, you can make some pretty nice diagrams.

If that count data is normalised, you can log2 the counts and use them for input into heatmap.2. I recommend Z-scaling too. Please read up on those packages and Google them, if you haven't done so already. You will be able to find some good examples on the internet.

ADD COMMENTlink written 9 weeks ago by Biogeek350
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