Question

DESeq2 ComputeSumFactors extract normalized counts

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herrmannmaria94 • 0

@herrmannmaria94-13966

Last seen 7.4 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 • 1.7k views

ADD COMMENT • link updated 7.4 years ago by Michael Love 43k • written 7.4 years ago by herrmannmaria94 • 0

score 0 · Answer 1 · 2017-09-16

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herrmannmaria94 • 0

@herrmannmaria94-13966

Last seen 7.4 years ago

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

ADD COMMENT • link 7.4 years ago herrmannmaria94 • 0

score 0 · Answer 2 · 2017-09-16

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Michael Love 43k

@mikelove

Last seen 16 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().

ADD COMMENT • link 7.4 years ago Michael Love 43k

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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! :)

ADD REPLY • link 7.4 years ago herrmannmaria94 • 0