scran/scater Normalized matrix
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Radek ▴ 90
@radek-8889
Last seen 4.1 years ago
Belgium

Hi!

I have a SingleCellExperiment Object. I used the following code to normalise my data:

sce <- scran::computeSpikeFactors(sce, general.use = FALSE)
scater::normalise(sce)

I would like to retrieve the normalised matrix of count afterwards but could not find a proper way to do it. Can someone tell me where is it stored in this object ? 

Thank you in advance!

scran scater normalized counts • 686 views
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Aaron Lun ★ 28k
@alun
Last seen 14 hours ago
The city by the bay

If you set return_log=FALSE in normalize, the "normalized counts" are available with normcounts(sce). Otherwise they're log-transformed and reported in logcounts(sce).

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Thank you ! 

 

 

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