Closed c2b2pss closed 1 year ago
the first mentioned group will be the test group (numerator in the fold-change) and the second mentioned will be the control (denominator). I.e. in the vignette example TeffNaive_U is the test and TeffMem_U is the control group
Hi,
In the vignette it is difficult to determine the sample order in the differential analysis. For example, if A is untreated and B is treated, and if I wanted to compare what is upregulted in treated compared to untreated or B/A, do I specifiy c(A, B) or c(B, A)?
I the T cells example
...shows the naive is first, so is naive the control ?
Similarly, in the "Differential Analysis" it is somewhat obscure what order "stimulus" is compared....
....what is 'differntial columns' and where is it derived from?
Thannks!