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davismcc / scaterPaperExtras

Discussion board for modifications to the scater paper
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Case Study #42

Closed LTLA closed 8 years ago

LTLA commented 8 years ago

... more than one cell ( or cell debris from other cells ) are being sequenced...

are -> is.

To normalize using ERCC spike-ins, you need to use computeSpikeFactors after setting isSpike:

isSpike(scDataQC) <- "spikes"
scDataQC_spikenorm <- computeSpikeFactors(scDataQC)

The get.spikes argument in computeSumFactors only controls whether spike-in transcripts are filtered out in the deconvolution method, it doesn't switch over entirely to spike-in normalization.

Consider using r Biocpkg("scater") for package references, which links straight to the scater BioC page.

davismcc commented 8 years ago

Cool - thanks for the clarification on computeSpikeFactors.

I didn't know about Biocpkg, so thanks for the heads up!

These are fixed now.