scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS

Question

[Bogdan]

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:

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,

-- bogdan

[shoujun.gu]

In general:

1. For most (if not all) unsupervised clustering algo, cluster numbers can be arbitrarily determined by adjusting algo params. Therefore, you can always keep any cluster number you want. However, packaged analysis platforms (such as seurat) may or may not provide the access to fine tune the internal algos. If the params are not provided by Seurat (although I think it's less likely), then you have to do the clustering by your own if you want to keep the number you want.

2. It's expected different treatment/time point may generate novel cell populations. I don't see any reason that the identity numbers in different treatment must remain the same.