Hello all, I am an undergraduate student running some RNA-seq expression data. I have been using idep for this analysis so far, but I wanted to customise the volcano plots a bit more using enhanced volcano. To do this I installed DESeq2 and enhanced volcano and got it set up with my data, but I am having difficulty getting the same graphs out of my results input. My analyses has two conditions, within each are two treatments such that the model is; ~condition1 + condition 2 + condition1:condition2

resultsNames outputs "intercept' "condition1_A_vs_B" "condition2_C_vs_D" "condition1A.condition2.C"

I have tried using the examples given in ?results, but I cannot replicate the idep analyses. When I run the results commands using contrast or list I get the results for the difference between A vs B, or C vs D. In idep my analysis allows me to select B vs A for D, D vs C for B and the interaction term. I am trying to mimmick this output specifically and I am not sure how to go about it, currently using the scripts below I am not getting any results that match any idep comparisons. I would very much appreciate the feedback of a more experienced individual. Thank you!

'''

res2 <- results(dds, list( c("condition2_C_vs_D", "condition1A.condition2C")), alpha = 0.05)

res1 <- results(dds, contrast = c("condition1", "A", "B"), alpha = 0.05)

'''

iDEP is not a Bioconductor package, so I'd recommend reaching out to their development team to find out what tables are being output by their software. They have an email here:

http://bioinformatics.sdstate.edu/idep/

gelabinfo AT gmail.com

Also on the iDEP publication you can find a contact email:

gexijin AT gmail.com

They also have a GitHub page:

https://github.com/iDEP-SDSU/idep