Question: transformed read counts in deseq2
0
gravatar for anna
17 months ago by
anna10
anna10 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 • 996 views
ADD COMMENTlink modified 17 months ago by Prakash2.1k • written 17 months ago by anna10
1

See answer here: retrieve normalised count data from DESeq2

ADD REPLYlink written 17 months ago by GenoMax95k

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 17 months ago • written 17 months ago by anna10

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

ADD REPLYlink written 17 months ago by swbarnes29.4k
2
gravatar for ATpoint
17 months ago by
ATpoint44k
ATpoint44k 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 17 months ago • written 17 months ago by ATpoint44k
1
gravatar for Prakash
17 months ago by
Prakash2.1k
India
Prakash2.1k wrote:

you can also extract normalized read count from dds object

res <- as.data.frame(counts(dds, normalized=TRUE))
ADD COMMENTlink written 17 months ago by Prakash2.1k
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