I am comparing differentially expressed genes (DEGs) between WT and KO samples. If I want to compare DEGs between conditions in a particular cluster I use FindMarkers
function of Seurat tool by indicating ident.1 and ident.2.
However if I wanted to compare overall DEGs between WT and KO samples and NOT specific to any cluster. How can I accomplish in Seurat or using other tool?
Thank you,
Hi,
From what I read in the documentation of
Seurat
, if you set bothident.1
andident.2
parameters toNULL
(the default by the way) it will do (according to the docs):if NULL, use all other cells for comparison
. See also the explanation on the Seurat vignettes/tutorials:If the ident.2 parameter is omitted or set to NULL, FindMarkers will test for differentially expressed
features between the group specified by ident.1 and all other cells
So, try something like:
I hope this answers your question.
António
Sorry, this will never work because you are comparing everything against everything, so obviously it'll not work. It only works when you want to compare one group against everything, then you can set the identity for that group
ident.1 = group
and the second identity group asNULL
-ident.2 = NULL
Sorry by the mistake.
Follow the solution provided by @jomo018
António
@jomo018 way worked. Thank you for your help, anyway.
@jomo018 way worked. Thank you for your help, anyway.