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

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6.8 years ago

Clara • 0

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?

RNA-Seq rna-seq R • 3.6k views

ADD COMMENT • link 6.8 years ago by Clara • 0

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Good evening Clara,

Italiana?

Something like this (?):

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...or this (?):

ADD REPLY • link 6.8 years ago by Kevin Blighe 88k

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How to get this result?

ADD REPLY • link 6.5 years ago by fatin nadhirah • 0

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ADD REPLY • link 6.5 years ago by Kevin Blighe 88k

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