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

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

r rna-seq enhancedvolcano plot
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written by camillab. • camillab.

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

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written by GenoMax GenoMax

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

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written by camillab. • camillab.

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

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written by GenoMax 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!

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written by GenoMax GenoMax

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. :)

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written by camillab. • camillab.

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.

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written by jared.andrews07 jared.andrews07

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