cohorts
cohorts copied to clipboard
Add `batch` identifier to cohorts & support estimation of batch effects
Would be useful to keep track of batch
identifiers so we can estimate batch effects as part of standard protocol.
Two parts to this request:
- [ ] add batch to sample meta-data
- [ ] implement method for summarizing batch effects, depending on type of sample
Possible methods for detecting batch effects:
- run combat on our samples to estimate batch effects from RNA-seq
- use SVA to try to estimate batch effects
- look for hierarchical clustering in DNA/RNA more generally