Question about inclusion of QC samples for batch correction

[Niveda-S]

Hi @ppedrioli ,

I have a dataset containing cohort and QC samples (digestion control and MS control), which are not the same biospecimen.
The QC samples we are using are for instrument QC and digestion QC and are reference standards that are commercially purchased healthy plasma samples. Cohort samples are also plasma samples and are from individuals with some biological phenotype (ex: heart disease). We are trying to run batch correction on both cohort and QC samples:

1. Should the batch correction be done together? If so, how would this impact the batch corrected numbers?
2. Alternatively, should we be running batch correction separately on QC and cohort samples?