transformed read counts in deseq2

Question: transformed read counts in deseq2

17 months ago by

anna • 10

anna • 10 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

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modified 17 months ago by Prakash • 2.1k • written 17 months ago by anna • 10

See answer here: retrieve normalised count data from DESeq2

ADD REPLY • link written 17 months ago by GenoMax ♦ 95k

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 REPLY • link modified 17 months ago • written 17 months ago by anna • 10

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

ADD REPLY • link written 17 months ago by swbarnes2 ♦ 9.4k

17 months ago by

ATpoint ♦ 44k

ATpoint ♦ 44k 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 COMMENT • link modified 17 months ago • written 17 months ago by ATpoint ♦ 44k

17 months ago by

Prakash • 2.1k

India

Prakash • 2.1k wrote:

you can also extract normalized read count from dds object

res <- as.data.frame(counts(dds, normalized=TRUE))

ADD COMMENT • link written 17 months ago by Prakash • 2.1k

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