Strange patterning in volcano plot
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!
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Can you try changing log scale to 10 instead of 2 on y axis? (-log10p instead of -log2p)
Looks basically the same. There is no y-axis transformation that rescues the plot.
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?