MA plot from Differential Expression between One Sample vs another · Biostar

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MA plot from Differential Expression between One Sample vs another

Hi all,

Is it possible to get MAplots when you only have foldchange and Expression values of the two samples of comparison(one vs one) ? I don't have replicates.So i only have FPKMS from 2 samples and their log2FoldChange.I know I don't have statistical significance but I still would like to have MA plots from log2Foldchange.

I have only seen MAplots from DESEQ2 results or edgeR results.

Any suggestions?

thanks,

Ron

rna-seq r differential-expression bioconductor

• 2,750 views • link

written 9.2 years ago by Ron

Well, if you have your FPKMs then you can simply plot it:

M = log2(FPKM1 / FPKM2)
A = 0.5*log2(FPKM1 * FPKM2)

require(LSD)
heatscatter(x = A, y = M)

• 0 views • link

written 9.2 years ago by ATpoint

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