Question: scran/scater Normalized matrix
0
gravatar for Radek
14 days ago by
Radek40
Belgium
Radek40 wrote:

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!

ADD COMMENTlink modified 14 days ago by Aaron Lun22k • written 14 days ago by Radek40
Answer: scran/scater Normalized matrix
0
gravatar for Aaron Lun
14 days ago by
Aaron Lun22k
Cambridge, United Kingdom
Aaron Lun22k wrote:

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).

ADD COMMENTlink modified 14 days ago • written 14 days ago by Aaron Lun22k

Thank you ! 

 

 

ADD REPLYlink written 14 days ago by Radek40
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