Closed denvercal1234GitHub closed 1 year ago
hi @denvercal1234GitHub,
Yeah, I mean, diffcyt
is methodology for performing analysis between conditions, not between clusters .. so, for finding marker genes, I suggest that you use something else. For example, you might be able to use the same findMarkers
function in scran
that is used in scRNA-seq marker DE detection, since the data used in CATALYST
is a SingleCellExperiment
object. I have actually never done this, because this is not typically the way that people do it for cytometry (generally, people pick markers to use in the first place). But, from a stats perspective, it should still work.
Cheers, Mark
Hi there,
The tutorial (https://www.bioconductor.org/packages/release/bioc/vignettes/diffcyt/inst/doc/diffcyt_workflow.html) is very useful, but it only shows how to perform the analysis between conditions.
I had performed clustering using
CATALYST
.Would you mind advising me how to adjust the codes, especially
diffcyt::createDesignMatrix
andcontrast
to identify differentially-expressed proteins (biomarkers) of a cluster compared to every other cluster, done for each cluster as in DEGs for scRNAseq analyses? Or is it not possible?Thank you for your help!