Question: DESeq2 ComputeSumFactors extract normalized counts
0
gravatar for herrmannmaria94
2.2 years 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 • 492 views
ADD COMMENTlink modified 2.2 years ago by Michael Love26k • written 2.2 years ago by herrmannmaria940
Answer: DESeq2 ComputeSumFactors extract normalized counts
0
gravatar for herrmannmaria94
2.2 years 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 2.2 years ago by herrmannmaria940
Answer: DESeq2 ComputeSumFactors extract normalized counts
0
gravatar for Michael Love
2.2 years ago by
Michael Love26k
United States
Michael Love26k 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 2.2 years ago by Michael Love26k

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 2.2 years ago by herrmannmaria940
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