Strange patterning in volcano plot

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3.6 years ago

Kathryn • 0

Hi all, I made a volcano plot from my DEseq2 output (DE on bulk RNAseq), and it has this weird "stripy" patterning. Does anyone know what this might indicate? As you can see from the plot, I didn't get very many DE genes in this comparison. I'm not sure if it's a data quality issue or if the two conditions I'm comparing are just incredibly similar.

Thanks!

enter image description here

RNAseq • 1.1k views

ADD COMMENT • link updated 3.6 years ago by cpad0112 21k • written 3.6 years ago by Kathryn • 0

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Can you try changing log scale to 10 instead of 2 on y axis? (-log10p instead of -log2p)

ADD REPLY • link 3.6 years ago by cpad0112 21k

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Looks basically the same. There is no y-axis transformation that rescues the plot.

enter image description here

ADD REPLY • link 3.6 years ago by Kathryn • 0

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Are you plotting the correct values? Scale seems to indicate negative -log10/2 p values (high p values) for most of the genes. Try filtering gene list by p-value (for eg. 0.05) and redraw the volcano plot. Can you post p-values (not log transformed) for few of the bottom most genes in the volcano plot?

ADD REPLY • link 3.6 years ago by cpad0112 21k

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