Question: How to create PCA plot and heatmaps using only significant genes in edgeR ?
0
gravatar for Björn
4 months 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 R • 390 views
ADD COMMENTlink modified 9 weeks ago by zx87545.6k • written 4 months ago by Björn30
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 weeks ago by WouterDeCoster34k
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 weeks ago by Kirill250

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 4 months ago by Kevin Blighe32k

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 4 months 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 4 months ago by Kevin Blighe32k

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 4 months ago • written 4 months ago by Carambakaracho570

A good point, Carambakaracho

ADD REPLYlink written 4 months ago by Kevin Blighe32k
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