teal with bioconductor 3.14

[nikolas-burkoff]

From https://github.com/insightsengineering/teal/issues/325 there is a problem running 4 teal tests.

@gogonzo can reproduce and will figure out which package the problem is coming from etc.

[gogonzo]

Issue submitted in the package repo. I think it's a problem of subsetByColData which does not handle NA like all subset functions.
waldronlab/MultiAssayExperiment#303

[gogonzo]

Discussion continuous in MAE repo. Also found an issue in S4Vectors which is not related with current one.

[gogonzo]

Ok, I'm done with this MAE author. Discussion does not make sense as he ignores strong reasons and tries to defend himself in the eyes of the user imputing general misconception. I suggest now to fix the teal as his proposition to add na.rm to subsetByColData is his "new idea" and there is still no issue created for this.

I think these should be possible instead of subsetByColData(<dataname>, <condition> & <condition>):

MAE_FILTERED@colData <- subset(MAE_FILTERED@colData, <condition> & <condition>)
# or
MAE_FILTERED <- subsetByColData(MAE_FILTERED, <condition & !is.na(varname1)> & <condition & !is.na(varname2)>)
# or 
MAE_FILTERED <- subsetByColData(MAE_FILTERED, which(<condition> & <condition>))

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edit:
Before we try to work-around let's wait for this