Gemma Eliminate `factors` and `factorValueObjects` from `BioAssayValueObject`

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For factorValueObjects, it's been replaced by simply factorValues.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

Oct 10 '23 23:10 arteymix

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

Oct 10 '23 23:10 oganm

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?

Oct 10 '23 23:10 oganm

I intend to remove both.

Oct 10 '23 23:10 arteymix

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

Oct 11 '23 01:10 oganm

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

Oct 11 '23 01:10 arteymix

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

Oct 11 '23 20:10 oganm

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

I'll get rid of factors though.

Oct 12 '23 15:10 arteymix

all good. poke me when it happens

Oct 13 '23 21:10 oganm