Bioconductor with RPKM counts or Raw counts
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kushshah ▴ 10
@kushshah-20393
Last seen 19 months ago
University of North Carolina, Chapel Hi…

I am performing a scRNA-seq analysis, and will be using the SingleCellExperiment library of Bioconductor to do so. The data for the project comes in both raw and log2(RPKM) formats. Is there a preferable format to use as the input for a SingleCellExperiment object? Does this object work well with RPKM input counts, or is it more advisable to just input raw reads and perform all basic normalization/QC starting from the raw reads? I would really appreciate any advice on this as I am new to Bioconductor and scRNA-seq analysis in general.

singlecellexperiment rpkm normalization qc • 340 views
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Aaron Lun ★ 27k
@alun
Last seen 17 hours ago
The city by the bay

I am performing a scRNA-seq analysis, and will be using the SingleCellExperiment library of Bioconductor to do so.

SingleCellExperiment doesn't do any analysis, it's just a data structure for single-cell data. If you want to do analysis, you should read the relevant workflows.

The data for the project comes in both raw and log2(RPKM) formats

What does "raw" mean? Raw counts?

Does this object work well with RPKM input counts

RPKMs are not counts.

or is it more advisable to just input raw reads and perform all basic normalization/QC starting from the raw reads?

Well, you'll need to align the reads first to get counts.

I would really appreciate any advice on this as I am new to Bioconductor and scRNA-seq analysis in general.

Don't use RPKMs for anything - except, perhaps, making plots of expression values.

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