Data for PCA plot in Deseq2

Is there a way of obtaining the actual data tables used for plotting the PCA, MA etc plots that is part of the output when running DeSeq2?

Hi @Edling,
this is the R script that runs behind the Galaxy tool wrapper: DESeq2 script. Could you specify which data tables are you interested to obtain?


Hi, thank you for that!
I have looked at the script and I think the tables/objects I would like to get out are the ones called dds and res in the script.
row 152: “generate_generic_plots ← function(dds, factors) {…”
row 176: “generate_specific_plots ← function(res, threshold, title_suffix) {”

However since I have run the DeSeq2 within Galaxy I don’t see a way to retrieve those specific objects without running the whole DeSeq2 in R. Any help with that would be very appreciated!

I would love to be able to do the whole thing in R myself, but looking at the script I don’t even understand where my count files go in… My R skills are not that good yet:-)
Also, I suspect this package take quite a lot of computer power to even work right?

Thank you,