Open jcasadogp opened 2 months ago
pseudoBulkDGE
is just a wrapper around edgeR or voom
, and the design matrix and coefficients can be interpreted in the same manner. In your case, if sce$donor_id
contains DON_A
and DON_B
, the matrix created by ~donor_id
will have an intercept and a donor_idDON_B
column that represents the log-fold change of DON_B
over DON_A
. So, if you set this as your coef
, your reported log-fold changes will be that of DON_B
over DON_A
.
FYI your label
setting is rather odd. It is intended to be the colData
column that represents the cluster/cell types, as pseudoBulkDGE()
will loop over all the different cell types and perform the specified DE analysis within each of them.
Hello,
I have the following code:
I want to compare two donors DON_A and DON_B with this code.
sce_list$current_sce$donor_id
gives me"DON_A", "DON_B", "DON_A", "DON_B"
andsce_list$current_sce
has the following dimensions:[1] 33904 4
I want to know if positive logFC values mean:
I have not found it in any documentation or other post/issue.
Thank you in advance!