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zentnerlab / TSRexploreR

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lfc_shrink not working in differential_expression #201

Closed perinom closed 2 years ago

perinom commented 2 years ago

Hi,

when calculating differential expression with

exp <- differential_expression(
  exp,
  data_type = "tsr", #"tss", "tsr", "tss_features", "tsr_features"
  comparison_name = comparison_name,
  comparison_type = comparison_type,
  comparison = comparison,
  shrink_lfc = TRUE)

it fails with

Error in (function (dds, coef, contrast, res, type = c("apeglm", "ashr", : coef %in% resultsNamesDDS are not all TRUE

shrink_lfc = FALSE works without issues.

PS Is there any chance of a future implementation of DESeq2 Likelihood Ratio Test for time-course analysis? (I can do it externally, of course, it'd just be handy to do everything from one interface (also because I love your QC/exploratory plotting functions)) :)

Thanks

perinom commented 2 years ago

Closing this one, it was my bad, I'm sorry!

Would still love the Likelihood Ratio Test for time-course analysis, though :)

Thanks again!