Question: Volcano plot with highlighted significantly up/down regulated genes with specific normalised reads value?
0
gravatar for camillab.
4 weeks ago by
camillab.30
London
camillab.30 wrote:

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

plot rna-seq enhancedvolcano R • 319 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by camillab.30
1

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

ADD REPLYlink written 4 weeks ago by genomax92k

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

ADD REPLYlink written 4 weeks ago by camillab.30

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

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax92k
1

@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!

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax92k

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. :)

ADD REPLYlink written 4 weeks ago by camillab.30
1

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.

ADD REPLYlink written 4 weeks ago by jared.andrews077.9k
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