DESeq2 ComputeSumFactors extract normalized counts
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@herrmannmaria94-13966
Last seen 4.0 years ago

I have a single cell RNA-dataset and I used the deconvolution method for normalization. Now I want to extract the matrix with all normalized counts but it is not working. I tried the following: 

sce <- computeSumFactors(sce, sizes=c(20, 40, 60, 400))

#Computing separate size factors for spike-in transcripts
sce <- computeSpikeFactors(sce, type="ERCC", general.use=FALSE)

#Applying the size factors to normalize gene expression
sce <- normalise(sce)
NormCounts = counts(sce, normalised = TRUE)

and the following error comes up:

> error in .local(object, ...) : unused argument (normalised = TRUE) 

it is also not working with normalized = TRUE.
Where is my mistake? Does someone have a solution for this?
Thank you in advance!

 

 

 

 

 

deseq2 normalization counts • 726 views
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@herrmannmaria94-13966
Last seen 4.0 years ago

I would like to only extract normalized counts, not log-normalized counts. Afterwards I want to use my TPM and logTPM calculation.

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@mikelove
Last seen 11 hours ago
United States
A few things: This isn't a function in DESeq2. The counts() function in DESeq2 has argument "normalized". And you don't need the function at all here if you just want to divide the columns by factors. You can use for example sweep().
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I am so sorry! I was so wiped out yesterday by a cold that I couldn't think of the obvious solution. Thank you for your answer! :)

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