Dear all,
I would like to ask you please for a suggestion : we do have a set of multiple scRNAseq experiments CTRL and STIM (in the same tissue) at 1, 2, 3, 4 months i.e:
CTRL1month, CTRL2months, CTRL3months, CTRL4months
STIM1month, STIM2months, STIM3months, STIM4months
and I have done the analysis by comparing :
a) CTRL1month vs STIM1month
b) CTRL2months vs STIM2months
however, for each comparison, the CLUSTER NUMBERS differ i.e. :
the CLUSTER_NUMBERS of the comparison :
a) CTRL1month vs STIM1month,
differ from the comparison :
b) CTRL2months vs STIM2months ...
is there any way we can keep the same CLUSTER NUMBERS over MULTIPLE COMPARISONS ?
in SEURAT, we've looked at the CONSERVED MARKERS between CLUSTERS in CTRL1 vs STIM1, and CTRL2 vs STIM2; the problem is that some of the clusters share too many conserved markers ...
thanks a lot,
-- bogdan
Thank you Aaron, for the quick and very informative reply ... As always, with big appreciation !
On an additional note, it is really exciting to see the developments of Muscat package too :
https://www.bioconductor.org/packages/devel/bioc/vignettes/muscat/inst/doc/vignette.html