I have a very fundamental question,
If we are doing differential gene expression analysis - for example - Between condition 1 vs Condition 2 via either Limma, DESeq or edgeR,
How to find out that the results that we got - up and down-regulated gene list - are deferentially expressed in Condition 1 vs 2 or they are differentially expressed in Condition 2 vs 1? meaning are they up or downregulated in Condition 1 as compared to condition 2 or they are up and down regulated in condition 1 as compared to condition 2?
I have done something like this in Limma:
design_matrix <- model.matrix(~0+matrix_model) colnames(design_matrix) <- c('Low', 'High') $contrasts Contrasts Levels High - Low Low -1 High 1 $design Low High 1 1 0 2 0 1 3 1 0 4 1 0 5 1 0 head(lm$coefficients) Contrasts High - Low A1BG -0.2442607336 A1CF -0.0004826392 A2M 0.4969213243 A2ML1 0.1609067551 A3GALT2 0.0154397887 A4GALT 0.0761423508
So - here - my conditions are - Low and High
How to find that the resulted gene list are up/down-regulated in High as compared to low or they up/down-regulated in Low as compared to High?
Looking forward to a valuable answer