Question: How to create PCA plot and heatmaps using only significant genes in edgeR ?
0
gravatar for Björn
21 months ago by
Björn40
Björn40 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 R • 1.3k views
ADD COMMENTlink modified 19 months ago by zx87549.1k • written 21 months ago by Björn40
2

Actually, this is not appropriate. If you are taking genes which you a priori know that are different between your samples and use those for a PCA then you will of course get a separation between your experimental groups. That's a circular analysis or "double dipping".

ADD REPLYlink written 19 months ago by WouterDeCoster43k
1

have a look at varistran R package, specifically at

y <- varistran::vst(counts, design=design)
varistran::plot_heatmap(y, n=50)
ADD REPLYlink written 19 months ago by Kirill270

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 21 months ago by Kevin Blighe56k

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 21 months ago by Björn40

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 21 months ago by Kevin Blighe56k

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 21 months ago • written 21 months ago by Carambakaracho2.0k

A good point, Carambakaracho

ADD REPLYlink written 21 months ago by Kevin Blighe56k
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