Question: how to apply volcano plot for genes predicting a phenotype
0
gravatar for adR
11 weeks ago by
adR50
adR50 wrote:

Hey guys, Is it an intuitive way using volcano plots genes that predict a continuous phenotype e.g BMI? I know it perfectly works for differentially expressed genes. I would be happy if someone can give me some directions. Best, Amare

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by adR50
0
gravatar for Kevin Blighe
11 weeks ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

Please elaborate on what you mean. It is not clear.

ADD COMMENTlink written 11 weeks ago by Kevin Blighe67k

Hi Kevin, I have a list of genes which predict a continuous variable BMI. I have no groups which I would like to compare but I would like to show positively and negatively correlated genes with BMI. For these purpose I am thinking to use regression estimate and pvalue. Do you think I can do that in volcano plot? Thanks for answering my question Best, AD

ADD REPLYlink written 11 weeks ago by adR50

Sure, you can regress each gene independently to BMI, but I am not sure why (or how) you want to do this in a volcano plot? Or, do you mean that you want to colour-shade the genes in the volcano plot based on BMI, in some way?

Perhaps one of the options in EnhancedVolcano can help? - https://github.com/kevinblighe/EnhancedVolcano

ADD REPLYlink written 11 weeks ago by Kevin Blighe67k

Yes I would like to colour shade the genes based on BMI! Thanks Kevin!

ADD REPLYlink written 11 weeks ago by adR50
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