Question

A problem about RNA-seq workflow:9 Time course experiments

1

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Guandong Shang ▴ 40

@shangguandong1996-21805

Last seen 2.1 years ago

China

In the RNA-seq workflow: gene-level exploratory analysis and differential expression 9 Time course experiments There is a sentence saying

We can furthermore cluster significant genes by their profiles. We extract a matrix of the shrunken log2 fold changes using the coef function:

But I do not see the lfcShrink fucntion in this

library("fission")
data("fission")
ddsTC <- DESeqDataSet(fission, ~ strain + minute + strain:minute)

So I am wondering whether there is no shrink for the coef(ddsTC)?

rnaseqgene • 1.1k views

ADD COMMENT • link updated 4.6 years ago by Michael Love 43k • written 4.6 years ago by Guandong Shang ▴ 40

score 2 · Answer 1 · 2020-05-25

2

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Michael Love 43k

@mikelove

Last seen 1 day ago

United States

Thanks for posting. That sentence needs to be fixed, it’s from an older version when coef() returned shrunken LFC. Now it only returns MLE. I’ll update the workflow text.

ADD COMMENT • link 4.6 years ago Michael Love 43k

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Thanks Dr.Love :). And If I want to get the shrunk log2FoldChange of coef(ddsTC), can I use below code ?

lapply(colnames(coef(ddsTC))[3:12], function(coef_name){
  result_lfc <- lfcShrink(dds = ddsTC, coef = coef_name,type = "apeglm")
  return(result_lfc$log2FoldChange)
}) -> betas

names(betas) <- colnames(coef(ddsTC))[3:12]
do.call(cbind,betas)

ADD REPLY • link 4.6 years ago Guandong Shang ▴ 40

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Yes, that works. I've updated the vignette to note that coef() provides MLE for coefficients.

ADD REPLY • link 4.6 years ago Michael Love 43k