Interaction terms in deseq2 and PCA plots

Uncategorized
1

Hi ,

I was wondering if design formulas like ~ genotype + light + genotype:light can be put in current galaxy deseq2 wrapper. Also in R one can just do a `~1 ` To get just the pca plot of all samples together.

These two things would be great for recommending galaxy at my workspace.

2

Hi @microfuge

I created an issue here DESeq2: add support for interaction effects · Issue #8907 · galaxyproject/tools-iuc · GitHub

But the implementation might take some time. If you have a colleague who can implement it, please share the following repo to contribute. We are happy to review :slight_smile:

Thank you for understanding!

Pavan

3

Meanwhile, please try mimicking your formula with some changes to the input for the current DESeq2 wrapper.

  • Use the input mode “Select contrast from sample sheet columns”
  • Have your count files in a collection. Name each of the samples.
  • Prepare a sample sheet file. In addition to light and genotype, add a column that defines the interaction. Something like the following
sample genotype light interaction
WT_dark_1 WT dark no
WT_dark_2 WT dark no
WT_light_1 WT light no
WT_light_2 WT light no
mutant_dark_1 mutant dark no
mutant_dark_2 mutant dark no
mutant_light_1 mutant light yes
mutant_light_2 mutant light yes

Then use the formula ~ genotype + light + interaction. I haven’t tested. That might work.