plot statistic values in a DEseq2 plotCounts plot
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@annehoffrichter-22701
Last seen 16 months ago
Germany

Hello,

I'm using DEseq2 on Illumina RNA-seq data. What I want to do is to create plots for my genes of interest, with the counts on the y-axis, and my sample types on the x-axis. This can be done very nicely with the function plotCounts(dds, gene=topGene, intgroup="timepoint", returnData=T) and subsequently calling the plot with ggplot2 . But now I would also like to add p-values showing the differences between my sample types. I tried using ggplot2 with geom_signif() and stat_compare_means() but even with the top gene from one of the results tables, I only get ns (non significant) plotted.

Is there an easy way to add significance levels to the output of plotCounts()?

Thanks for your help, Anne

deseq2 plotCounts pvalues RNAseq • 1.6k views
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@mikelove
Last seen 3 days ago
United States

This downstream plotting of DESeq2 output is up to you. I don't think it will be useful to try any of those geom's or stat's as they are for simple group testing, and for a number of reasons, the DESeq2 model is not doing the same inference as these.

So you're on your own. If you're new to ggplot2, they have a lot of online documentation, or you can consult someone in your group/department/institute who has more experience.

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