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PavlidisLab / Gemma

Genomics data re-analysis
Apache License 2.0
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Eliminate `factors` and `factorValueObjects` from `BioAssayValueObject` #895

Open arteymix opened 1 year ago

arteymix commented 1 year ago

The RNA-Seq pipeline will stop using factors in its next release.

For factorValueObjects, it's been replaced by simply factorValues.

@oganm will this affect the R or Python packages?

oganm commented 1 year ago

It should be fine as far as I can see. factors were never processed it seems but i could use an example where factors currently appears

oganm commented 1 year ago

ok found one looking at https://gemma.msl.ubc.ca/rest/v2/datasets/GSE49712/samples. it does appear that factorValueObjects are already present. i assume the change will only be removal of factors?

arteymix commented 1 year ago

I intend to remove both.

oganm commented 1 year ago

ah i see, then i'd have to introduce a fix but it's not a very large one. just let me know when it happens and i'd prefer if it happened before Oct 18 or after Oct 25 so i'm not blind sighted with the bioconductor release

arteymix commented 1 year ago

@oganm which ones are you using in Gemma.R?

oganm commented 1 year ago

Just the factor Value Objects. factorValues are also used when they are currently present

arteymix commented 1 year ago

Ok, start using factorValues, I'll keep the other one for backward compatibility.

I'll get rid of factors though.

oganm commented 1 year ago

all good. poke me when it happens