Closed lw157 closed 1 year ago
Hi @lw157
For the moment, I recommend running this in two separate analyses (so one analysis per contrast, each with "C" as group name).
Hi @lw157
For the moment, I recommend running this in two separate analyses (so one analysis per contrast, each with "C" as group name).
Thanks a lot, Robin. I will run them separately with same group name.
Just one more question. I found the results (LR pairs) of "dividing by group number" is different from NOT dividing. In this case, should I divide by 4? e.g. ((C-D)-(A-B))/4 (or (C-D)/2-(A-B)/2? ), or just go with (C-D)-(A-B) ?
From multinichenetr tutorials, there is no dividing for the anti-PD1 case, but from limma manual, it seems they suggest to use "divide by group #" (page 47 from https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf ).
Thanks again.
All best, Liuyang
Hi @lw157
In the MultiNicheNet code of writing out your contrasts, we use the way described in 9.5.2 (without dividing when comparing equivalent groups), and not the way described in 9.5.4.
Thanks a lot, Robin. This is really helpful. I will close this post.
Hi, I would like to make a contrast table for 4 groups, A, B, C, D. But I have trouble for the "group" in contrast_tbl.
From the tutorial, the group must be chosen from A, B, C, D. Here I set group "C" for "(C-D)-(A+B)", but for (C-A)+(D-B), what should I set as C2 is not from ABCD.
Liuyang