Error using DESeq2 Wald test for `drop_uninformative_genes()`

NathanSkene / EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

https://nathanskene.github.io/EWCE/index.html

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Error using DESeq2 Wald test for `drop_uninformative_genes()` #81

Closed cyouh95 closed 1 year ago

cyouh95 commented 1 year ago

1. Bug description

Getting below error when specifying dge_method = 'deseq2' and dge_test = 'Wald' for drop_uninformative_genes().

Console output

Error in DESeq2::DESeq(dds, test = test, reduced = ~1, parallel = no_cores >  : 
  'reduced' ignored when test='Wald'

Expected behaviour

It seems the reduced argument mentioned in the error message is only applicable to the default dge_test = 'LRT'.

bschilder commented 1 year ago

Hi @cyouh95 ,

It seems this argument was exposed to users in error. This feature has not yet been fully tested and thus shouldn't be used (EWCE only supports "limma" currently).

Second, in the future could you please fill out the rest of the bug report template? seems you're missing most of it, which makes it hard for us to address any bugs.

bschilder commented 1 year ago

@cyouh95 I've just fixed the exposed argument issue on the master branch (will need to discuss with @Al-Murphy to see what to do about the older branches). please use the defaults until we fully release these features. apologies for the confusion.

Best, Brian