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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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Which data type for clustering #85

Closed mkrzak closed 5 years ago

mkrzak commented 5 years ago

Hi,

I have a question concerning the type of counts that are favorable for SC3 clustering. In the example there are log transformed FPKM . Do you think that method would work well with raw counts, UMIs or CPM ?

Best, Monika

wikiselev commented 5 years ago

Hi Monica, sorry for a late reply. SC3 will work with anything (but without negative values) you give it, but it is recommended to do a library size normalisation and log transformations for most of the scRNAseq methods.

Very sorry for such a late reply.

mkrzak commented 5 years ago

Dear @wikiselev Thank you very much for your answer, it is still useful for me. Best, Monika