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:
CTRL_1month, CTRL_2months, CTRL_3months, CTRL_4months
STIM_1month, STIM_2months, STIM_3months, STIM_4months
and I have done the analysis by comparing :
a) CTRL1_month vs STIM_1month
b) CTRL2_months vs STIM_2months
however, for each comparison, the CLUSTER NUMBERS differ i.e. :
the CLUSTER_NUMBERS of the comparison :
a) CTRL1_month vs STIM_1month,
differ from the comparison :
b) CTRL2_months vs STIM_2months ...
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 many conserved markers ...
thanks a lot,