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statOmics / msqrob2

Implementation of the MSqRob analysis of differentially expressed proteins using the Features infrastructure
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Temporary fix to replace the filterFeatures error #42

Closed StijnVandenbulcke closed 2 years ago

lgatto commented 2 years ago

Could you provide some details about this error? I am not aware of any issues with filterFeatures().

StijnVandenbulcke commented 2 years ago

On the latest bioconductor version the cptac vignette did not run anymore, see: http://bioconductor.org/checkResults/devel/bioc-LATEST/msqrob2/

Quitting from lines 144-145 (cptac.Rmd) Error: processing vignette 'cptac.Rmd' failed with diagnostics: 'pe' is/are absent from all rowData.

filterFeatures was looking for a column named pe in the rowdata as it is referenced after the %in% operator. I did not find a solution while using the filterFeatures, so i i changed it temporarily so that the vignette is able to run.

lgatto commented 2 years ago

@cvanderaa - does this ring a bell? Could this be related to the new keep argument?

milanmlft commented 2 years ago

The problem seems to be due to the way the filtering formula was specified in the msqrob2 vignette:

pe <- filterFeatures(pe, ~ Proteins %in% smallestUniqueGroups(rowData(pe[["peptideLog"]])$Proteins))

This then gets passed on to QFeatures:::filterFeaturesWithFormula() which checks whether all variables are present in the rowData using https://github.com/rformassspectrometry/QFeatures/blob/2cc148ae924bc2bf6da9f228bb0467f196875dd6/R/QFeatures-filter.R#L287

But, since

ff <-  ~ Proteins %in% smallestUniqueGroups(rowData(pe[["peptideLog"]])$Proteins)
all.vars(ff)
#> [1] "Proteins" "pe"

we get the error, because there is no "pe" variable in the rowData.

Not sure why this problem didn't occur before and whether this should be addressed in the QFeatures package. If so, we could open a new issue in QFeatures.

cvanderaa commented 2 years ago

Yes sorry this indeed rings a bell! The issue should be solved in one of my branches: https://github.com/rformassspectrometry/QFeatures/commit/0ba8d4bfb346ad64b3750ba6dd39d4672d3ac4b1

I will make a PR to QFeatures as quick as possible to make this accessible to msqrob2.

lgatto commented 2 years ago

A fix has just been pushed to Bioc devel. Is also available from the github repo.