Question: How to create PCA plot and heatmaps using only significant genes in edgeR ?
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gravatar for Björn
3 days ago by
Björn30
Björn30 wrote:

How to create PCA plot and heatmaps using only significant genes in edgeR ? I have 10 genes at signficant different levels between comparison groups. How can I create PCA and heatmaps with only those 10 genes. Suggestions on R code will be appreciated !

heatmaps edger pca • 114 views
ADD COMMENTlink modified 3 days ago • written 3 days ago by Björn30

Hey Björn, Have you not searched for how to do this? There is extensive material across the World Wide Web (and on Biostars) about how to do this. Kevin

ADD REPLYlink written 3 days ago by Kevin Blighe23k

Thanks Kevin, I used standard edgeR code for PCA but wanted to create PCA for 50 DE genes out of 2000. Use only 50 genes out of 2000 in PCA plot.

ADD REPLYlink written 3 days ago by Björn30

Okay. You could just filter your logCPM data to include only your genes of interest, and then regenerate the PCA bi-plot. I have also put code here: A: PCA plot from read count matrix from RNA-Seq

ADD REPLYlink written 3 days ago by Kevin Blighe23k

wouldn't it be more or at least equally interesting to see where the data is in the PCA on all data?

ADD REPLYlink modified 3 days ago • written 3 days ago by Carambakaracho350

A good point, Carambakaracho

ADD REPLYlink written 3 days ago by Kevin Blighe23k
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