Volcano plot with highlighted significantly up/down regulated genes with specific normalised reads value?

Question

[camillab.]

Hi,

Maybe a naive question but I would like to know if and how is possible to have a the volcano plot (potentially with EnhancedVolcano since it's a great package) with highlighted not only significant up/down regulated genes but also those genes that have normalised reads (FPKM) higher than a specific value:

• pvalue < 0.05 + log2FC >1 + FPKM >6
• pvalue < 0.05 + log2FC < -1 + FPKM >6

and if not, which plot should I use?

Thank you in advance!

Camilla

[GenoMax]

Please post this over on Bioconductor support site (@Kevin prefers to have questions posted there).

[camillab.]

But is it not more confusing if I post it in both sites?

[GenoMax]

I will go ahead and close this question. In future please remember to post only on bioconductor.

[GenoMax]

@Kevin Blighe prefers support questions to be posted to https://support.bioconductor.org/ if you are specifically asking about `EnhancedVolcano`.

Note: I reopened this question based on the explanation below. Will not delete this comment since it will make the comments below this invisible for normal users.

Cheers!

[camillab.]

Hi ! I don't disagree. I just want to specify that I thought was better to put it here since I did not ask only about the volcano plot but I have also asked if there were any packages / type of plot I don't know that could give me the result desired. :)

[jared.andrews07]

You could do this with EnhancedVolcano easily enough, or you may want to consider an MA plot, which is quite good for displaying the expression cutoff.