I am having troubles interpreting the results after running
same.dir = TRUE, on a log2 fold changes that were obtained after an analysis with DESeq2. I am not sure what the meaning of up- and downregualted pathways is. Are this pathways where all the genes are up- or downregulated? Additional, up- or downregulated compared to what?
I know that the sign of the log2 fold changes reflect in which condition the expression is up- or downregulated compared to chosen control. In my case, a positive log2 fold change corresponds to a gene that is more expressed in diseased cells compared to healthy cells, while a negative log2 fold change corresponds to a gene that is less expressed in diseased cells compared to healthy cells.
Thanks in advance.