How to make a Scatterplot and a DE gene list from ballgown results?

Question

[Clara]

Hi and thanks for reading.

I have the ballgown element with e.ctab, t.ctab, i.ctab, e2t.ctab, i2t.ctab data for 4 samples (2 replicas of mutant and 2 replicas of control).

Well, I'm not able to process the data to make scatterplots and to extract the DE gene list.

I have now 2 variables: results_genes (with fc, pval, qval, mean and ids) and gene_expr (with the FPKM of each sample).

The scatterplot I want to do is one with all genes expressed and then, select and colour the activated genes (fc > 2) and the repressed ones.

How can I get there?

[Kevin Blighe]

Good evening Clara,

Italiana?

Something like this (?):

--------------------------------------

...or this (?):

[fatin nadhirah]

How to get this result?

[Kevin Blighe]

The volcano plot code is on my GitHub page: https://github.com/kevinblighe/EnhancedVolcano