I have questions about the use of numeric contrast and lfcshrink.

I set up the dds object using:

dds <- DESeqDataSetFromMatrix(countData = counts, colData = metadata, ~ Sex + genotype * treatment)

Model matrix was calculated using:

mod_mat <- model.matrix(design(dds, data = colData(dds))

Model matrix first line and last line show:

I defined my numeric contrasts and comparison as follows:

define_contrasts <- function() {
  wt_igg <- c(1, 0, 0, 0, 0)
  ko_igg <- c(1, 0, 1, 0, 0)
  wt_pltd <- c(1, 0, 0, 1, 0)
  ko_pltd <- c(1, 0, 1, 1, 1)

  list(
    contrast_igg = ko_igg - wt_igg,
    contrast_pltd = ko_pltd - wt_pltd,

    contrast_wt = wt_pltd - wt_igg,
    contrast_ko = ko_pltd - ko_igg,

    twoway_treatment = (ko_pltd - wt_pltd) - (ko_igg - wt_igg),
    twoway_genotype = (ko_pltd - ko_igg) - (wt_pltd - wt_igg)
  )
}; all_contrasts <- define_contrasts()

I extracted the results (using specific numeric contrast comparison) and performed lfcshrink using ashr method as it allows for the use of numeric contrasts.

for (contrast_name in names(all_contrasts)) {
contrast_vector <- all_contrasts[[contrast_name]]
res <- results(dds, contrast = contrast_vector, alpha = 0.05)
res <- lfcShrink(dds, contrast = contrast_vector, res = res, type = "ashr")}

My questions are:

1. Based on my design formula, shall I set the coef for Sex at 0 if my goal is to remove the effect of sex/gender on my datasets? I'm asking cause I realize that F was ref level and I wasn't sure if setting coef for Sex at 0 is the right way to remove effect of sex/gender.
2. Do the numeric contrast subtractions make sense logically?
3. I choose ashr method for lfcshrink because it allows for the use of numeric contrasts and also because in some comparisons there are >1 coef 'in use' and apeglm only allows for the use of a single coef for lfcshrink. Did I understand these correctly?

Apologies in advance if many questions seem very naive as I am learning these on my own using online resources to try to analyse my scrna-seq data and I don't have much experiences/

For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statistician or someone familiar with linear models in R. The way DESeq2 and lfcShrink work is the same for any linear model built in R.