Hello all thanks for the help in advance I have 4 groups, two different cell lines (w and b) which were non-treated (nt) and treated (t). I wanna find genes that are uniquely DE in the w-treated group compared to the other groups.
Code should be placed in three backticks as shown below
contr.matrix <- makeContrasts( unique_w_treated = w_t- (w_nt + b_nt + b_t)/3, levels = colnames(design)
so, when I do this I get 164 DE genes, but doesn't make much sense to me because when I compare w_t vs w_nt alone, I only have 13 DE genes? Am I doing something wrong? Thanks
sessionInfo( ) R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:  grid stats4 parallel stats graphics grDevices utils datasets methods base