Question: Bioconductor with RPKM counts or Raw counts
0
gravatar for kushshah
8 months ago by
kushshah10
University of North Carolina, Chapel Hill, USA
kushshah10 wrote:

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.

ADD COMMENTlink modified 8 months ago by Aaron Lun25k • written 8 months ago by kushshah10
Answer: Bioconductor with RPKM counts or Raw counts
2
gravatar for Aaron Lun
8 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

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.

ADD COMMENTlink written 8 months ago by Aaron Lun25k
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