Hi, I read many time DESeq2 doc(https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#differential-expression-analysis) specifically section 'Interaction'. There is a lot of great explanations. I see the example using a design very similar to what I use :
design ~genotype + condition + genotype:condition.
I also searched and read (https://rstudio-pubs-static.s3.amazonaws.com/329027_593046fb6d7a427da6b2c538caf601e1.html) that is very intersting but still haven't found the answer to my question.
I read also this(https://www.statisticshowto.com/wp-content/uploads/2016/09/2101f12WaldWithR.pdf) which is very close to what I need, but in this case it shows Wald test for 1 factors with 2 levels. And I want to know how calculation is done with 2 factors...
I read DESeq2 code, in particular about 'makeWaldTest' (github: https://github.com/mikelove/DESeq2/blob/master/R/results.R; lines 1031 to 1048) which is totally useful to see how Wald test is performed when you have 1 factor, like just a condition with for example Tumor versus Normal. but with those 2 doc and all my other searches , I still haven't figure out the answer for one question I have:
What I am searching for is : How is it calculated, how the Wald test is performed when you have 2 factors with 2 levels each, with a design like we have upper here? Like you want your comparison to be for example: ( Genotype1(Tumor/Normal) ) / (Genotype2(Tumor/Normal))
Many thanks for your help!
Hi, thank you very much for this interesting answer. I did more reading and thinking after I read your answer to deeply understand. Would it be correct to say that it does a 'Multiple Linear Regression' to get the coefficients that you explain here, that are use for the following steps in the DESeq2? What I mean is if I understand correctly, for 1 factor with 2 levels, it does a linear regression to get the coefficient. So I would like to confirm if I understand correctly what is done when we use 2 factors with interaction, is it Multiple Linear Regression that is used to estimate coefficients? Thank a lot for your time and help again.
Hmm, well DESeq2 is a GLM but is conceptually similar to multiple linear regression. See the DESeq2 paper if you want more details on the model and how the parameters are fit.
Absolutely, I saw GLM in your paper. I was sure it applies to 1 factor. I understand is also for more factors also. Many thanks.