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alanocallaghan / scater

Clone of the Bioconductor repository for the scater package.
https://bioconductor.org/packages/devel/bioc/html/scater.html
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Issue with runTSNE and deprecated parameter, i.e. use_dimred? #163

Closed gabrielet closed 2 years ago

gabrielet commented 2 years ago

This is not actually a question but rather an issue I found out which I posted on another website.

Briefly, the problem arise when using runTSNE and the deprecated parameter use_dimred. Indeed, it is still possible to use the parameter, for the reason explained in the link I provided, use_dimred. It is definitely likely that someone using a not-so-old pipeline might still be using such parameter without any warning or error thrown by the running code. Problem is, its use is misleading and will surely lead to wrong conclusions once the generated tSNE is used to decide how to proceed with downstream analyses.

I would suggest to add a warning or something to point out that with the newest versions of the package, the use of use_dimred is deprecated while 'dimred` must be used instead.

alanocallaghan commented 2 years ago

Added a warning that I may end up removing in later versions