Question: transformed read counts in deseq2
0
gravatar for anna
6 months ago by
anna0
anna0 wrote:

How can I extract the normalized and transformed read counts in deseq2 which are used to calculate the log fold change?

read counts deseq2 data • 294 views
ADD COMMENTlink modified 6 months ago by Prakash1.8k • written 6 months ago by anna0
1

See answer here: retrieve normalised count data from DESeq2

ADD REPLYlink written 6 months ago by genomax78k

i've tried that function but the data are not transformed. Also i've read that the function (rlog) retrieve the transformed counts but i can't get any result by doing this: write.csv(as.data.frame(rlog(dds, blind=TRUE, fitType = "parametric")), file="transformed.csv")

ADD REPLYlink modified 6 months ago • written 6 months ago by anna0

What function exactly did you try? rlog values are not used for calculating log fold changes.

ADD REPLYlink written 6 months ago by swbarnes27.5k
2
gravatar for ATpoint
6 months ago by
ATpoint30k
Germany
ATpoint30k wrote:
rld <- rlog(dds)
assay(rld)

How to export rld (rlog) or vsd values from DESeq2?

As far as I know essentially all DESeq2 object types are SummarizedExperiment containers and therefore can be accessed with assay to select counts. data.frame(rlog) is not possible as you first have to access the counts inside the SummarizedExperiments container.

ADD COMMENTlink modified 6 months ago • written 6 months ago by ATpoint30k
1
gravatar for Prakash
6 months ago by
Prakash1.8k
India
Prakash1.8k wrote:

you can also extract normalized read count from dds object

res <- as.data.frame(counts(dds, normalized=TRUE))
ADD COMMENTlink written 6 months ago by Prakash1.8k
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