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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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SC3 with Batch Correction #92

Closed hkarakurt8742 closed 5 years ago

hkarakurt8742 commented 5 years ago

Hello, I want to use SC3 for data sets from multiple batches. I use fastMNN() function of Scran package for batch normalization but it does not effect logcounts, it just creates a reduced dimension "MNN" that shows the corrected data. How can I use SC3 with these values? Can I create a new SingleCellExperiment with MNN matrix and use SC3 on that matrix? MNN matrix includes negative values so I know I should not use gene_filter parameter as TRUE.

Thank you in advance.

wikiselev commented 5 years ago

Hi, you can always copy your corrected matrix to logcounts, so no need to create a new object. Or if you care about logcounts, then yes, it would be a good idea to create a separate object.

However, I think SC3 won't work well with negative values (as majority of other scRNAseq methods), so cannot guarantee a good result.