lfcShrink function in DEseq2 is giving me an error

Question

[Fawzi Yassine]

Hi,

lfcShrink function in DEseq2 is giving me the following error: Error in lfcShrink(dds = dds, res = res_deseq2) : res should be a DESeqResults object, for GRanges output use 'format'

My code is:

dds = DESeqDataSetFromMatrix(countData = count_data, colData = pheno_data, design = ~ genotype)
dds = DESeq(dds)

res_deseq2 = results(dds, contrast = c("genotype", "Friedreichs_ataxia","Control"), tidy = TRUE)
lfcShrink_res_deseq2 = lfcShrink(dds=dds, contrast = c("genotype", "Friedreichs_ataxia","Control"), res = res_deseq2)

My DEseq2 is 1.2.22

[Kevin Blighe]

Is your version v1.2.22 or the current version (as of writing, 18th March 2019), v1.22.2?

What is the output of:

typeof(res_deseq2)
class(res_deseq2)

?

Also, please paste the output of sessionInfo()

Answer 1

[ATpoint]

Using results with tidy=T will coerce it to data.frame (see ?results), but lfcShrink wants GRanges as suggested in the error message. Use tidy=F or don't specify it at all as GRanges is default.

Error in lfcShrink(dds = dds, res = res_deseq2) : res should be a DESeqResults object, for GRanges output use 'format'

[Fawzi Yassine]

Problem solved. Please, can you check this https://www.biostars.org/p/370268/?

[GenoMax]

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