Mavolcanoplot Warning: Negative values are ignored problem.

I want to use volcano plot to find differentially expressed genes but when I use mavolcano command for it, it says Negative values are ignored. How can I add these negative values to my volcano plot?

Thank you.

Answer 1

[Tim DeFreitas]

mavolcanoplot assumes the input data are gene expression values, and a negative expression value is assumed to be invalid, because the baseline expression value for any gene is 0, and can only increase.

Some datasets, however, are normalized to a reference and are given as the log2 fold change compared to that reference. This data must be "de-normalized" back to original values in order to be used with mavolcanoplot. If X is my input vector, my raw data would be 2.^X. You can use the de-normalized data directly with the 'LOGTRANS' option, or convert the raw data back to log scale with log2.