Assay selection error within multiple functions

[LPotter21]

Good afternoon all,

When working through the batch correction options in the standR pipeline, I have spotted an error in a few different functions relating to the assay pulled. In our data, we are utilizing quantile normalized counts, which becomes the 3rd assay in the spe object, after counts and logcounts.

When calculating the negative control genes using findNCGs, while n_assay is a variable in the function, it is not utilized; instead, logcounts is always pulled for this calculation.

Additionally, when using geomxBatchCorrection, while n_assay does work to pull and correct the data from the selected assay, it always writes the data to the logcounts assay, leaving uncorrected data in the original slot. This is true whether the method is RUV4, Limma, or RUVg.

Currently, I have not searched through any additional functions to see if there are other instances of assay choice being overridden.

[ningbioinfo]

Hi @LPotter21 , yes you're correct for the findNCGs, that's a small bug in the function, I'll fix it right away thanks for pointing that out!
For the geomxBatchCorrection, I got raise for this before, I'll make an update with extra parameter where you can choose to store it instead of overwrite.

[ningbioinfo]

Hi @LPotter21 , in the devel version of standR (i.e. the github one and will be in the next version of BioC release), the findNCGs is now fixed, and there is a new parameter in geomxBatchCorrection called outAssay which you can specify to new assay slot (by default is still logcounts).