number of cell clusters in scRNA-seq
1
0
Entering edit mode
Bogdan ▴ 670
@bogdan-2367
Last seen 13 months ago
Palo Alto, CA, USA

Dear all,

considering some of the pipelines that are described in https://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html, would you please let me know, how could I modify the clustering parameters ("the resolution") in order to increase/or to decrease the number of CLUSTERS ?

thanks a lot,

  • bogdan
scran scater sc3 • 1.8k views
ADD COMMENT
1
Entering edit mode
Aaron Lun ★ 28k
@alun
Last seen 9 hours ago
The city by the bay

If you're using graph-based clustering methods, increase k to decrease resolution (i.e., bigger and fewer clusters). If you're using hierarchical clustering, you can fiddle with a range of cutreeDynamic parameters, starting with deepSplit. Sometimes dropping minSize is also helpful if you have lots of small clusters that are being forcibly merged to satisfy the minimum size requirement.

ADD COMMENT
0
Entering edit mode

Hi Aaron, thanks a lot for the quick reply ! very much appreciate it !

If i may add an additional question, it is related to filtering of cells, and normalization, before performing the clustering :

you'd always recommend data FILTERING (of cells, and genes) before NORMALIZATION (and NOT a NORMALIZATION step before FILTERING), correct ? thanks a lot !

ADD REPLY
0
Entering edit mode

Yes, I would filter out low-quality cells before normalization. Note that computeSumFactors() will automatically filter out genes for you, so that's not necessary; other normalization methods (e.g., library size normalization, spike-in normalization) are robust to low-abundance genes so they don't care.

ADD REPLY
0
Entering edit mode

it is great to have your comments; thank you, Aaron !

ADD REPLY

Login before adding your answer.

Traffic: 851 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6