Question: How to create PCA plot and heatmaps using only significant genes in edgeR ?
0
gravatar for Björn
11 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 • 810 views
ADD COMMENTlink modified 9 months ago by zx87547.5k • written 11 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 9 months ago by WouterDeCoster39k
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 9 months ago by Kirill260

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 11 months ago by Kevin Blighe44k

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 11 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 11 months ago by Kevin Blighe44k

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 11 months ago • written 11 months ago by Carambakaracho1.2k

A good point, Carambakaracho

ADD REPLYlink written 11 months ago by Kevin Blighe44k
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