Question: DESeq2 ComputeSumFactors extract normalized counts
0
gravatar for herrmannmaria94
21 months ago by
herrmannmaria940 wrote:

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!

 

 

 

 

 

normalization deseq2 counts • 424 views
ADD COMMENTlink modified 21 months ago by Michael Love24k • written 21 months ago by herrmannmaria940
Answer: DESeq2 ComputeSumFactors extract normalized counts
0
gravatar for herrmannmaria94
21 months ago by
herrmannmaria940 wrote:

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

ADD COMMENTlink written 21 months ago by herrmannmaria940
Answer: DESeq2 ComputeSumFactors extract normalized counts
0
gravatar for Michael Love
21 months ago by
Michael Love24k
United States
Michael Love24k wrote:
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 COMMENTlink written 21 months ago by Michael Love24k

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 REPLYlink written 21 months ago by herrmannmaria940
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