scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
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Bogdan ▴ 670
@bogdan-2367
Last seen 13 months ago
Palo Alto, CA, USA

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

scRNA-seq • 891 views
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Aaron Lun ★ 28k
@alun
Last seen 15 hours ago
The city by the bay

You won't be able to force the clustering algorithm to give you the same cluster number for the "same cell type" across batches. I mean, the clustering algorithm working on one batch of data doesn't even know about the other batch, so how can it possibly keep the numbers consistent? And what is a cell type anyway?

Just figure out which clusters match up to each other. There are multiple ways to do this:

  • batchelor (in the BioC-devel version, 1.3.9) has a clusterMNN() function that can be used to do mutual nearest neighbor matching on clusters. You can extract across-batch groups of related clusters from the metadata() of the output.
  • SingleR has a matchReferences function, just feed it two datasets with some sort of annotation and watch it construct a matrix of mutual assignment probabilities. You can visualize this on a heatmap to easily figure out which clusters match between batches.

And there's no need for all-caps, I can read perfectly fine without them.

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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

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