Fix joint rpca handling

[sabujcb]

No description provided.

[sabujcb]

#831 @antagomir

[TuomasBorman]

Thanks! See comments.

[antagomir]

Hi @sabujcb - add justifications where you can and where not sure you can flag those for discussion.

[sabujcb]

I checked everything, and all changes were taken into account.

[antagomir]

Checks are still failing with this:

`> mae[[2]] <- transformAssay(

• mae[[2]], assay.type = "mtx", method = "rclr", impute = FALS)
  

Error: object 'FALS' not found
Execution halted
`

-> did you try & run these with the code before PR:

R CMD build mia 
R CMD check mia_a.b.c.tar.gz
R CMD BiocCheck mia_a.b.c.tar.gz
R CMD INSTALL mia_a.b.c.tar.gz 

[sabujcb]

Checks are still failing with this:

`> mae[[2]] <- transformAssay(

• mae[[2]], assay.type = "mtx", method = "rclr", impute = FALS)
  

Error: object 'FALS' not found Execution halted `

-> did you try & run these with the code before PR:

R CMD build mia 
R CMD check mia_a.b.c.tar.gz
R CMD BiocCheck mia_a.b.c.tar.gz
R CMD INSTALL mia_a.b.c.tar.gz 

I executed PR from RStudio terminal and not exactly using these commands.