Please help with edgeR script

Question

[bioinformatics.girl]

Having trouble converting this into an instance where I am not comparing the cell types but rather the genotypes (CKO and FLOX).

I have already subsetted for the excitatory population and need to compare the up/downregulation occurring at the level of the biological replicates.

https://bioconductor.org/packages/release/bioc/vignettes/Glimma/inst/doc/single_cell_edger.html

Perhaps, I am missing something here, but how would you compare the genotypes using the script here. And I cannot really use the "cell_types" argument, since all of the cell types found in this cluster would clearly be excitatory since it is an excitatory cell population...

Thank you in advance!

Answer 1

[jv]

I don't use edgeR much myself, but it looks like you would replace cell_types with genotype when running DGEList, e.g.,

pb_dge <- DGEList(
    counts = pb_counts,
    samples = pb_sample_anno,
    group = pb_sample_anno$genotype)

Of course, you first have to define genotype in pb_sample_anno