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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Input from Seurat Object #93

Open andrewjkwok opened 5 years ago

andrewjkwok commented 5 years ago

Hi,

It seems that the two functions CreateSinglerObject and CreateSinglerSeuratObject both create a singler object, and the latter additionally makes a seurat object. However, if I've used Seurat 3.0 to integrate multiple datasets via canonical correlation analysis, can I then use the integrated dataset in singler? I can't seem to get that to work because my output from the CCA is part of a Seurat object which singler does not seem to accept.

Many thanks.

dviraran commented 5 years ago

Hi,

Did you look at case 2 here? I think it should answer your question. Do not input the CCA data, just the raw counts (in Seurat 3.0 its called RNA@counts).

Best, Dvir

biobug16 commented 5 years ago

Hi Dvir, In order to use the case 2, how can we generate the raw counts from the integrated dataset (which is having 5 samples in my case)? I'll really appreciate if you can elaborate this.

Thanks