Batch correction
Build a docker image, then run like so:
docker run --rm -v `pwd`:/data jeltje/combat -b batch_info.tsv -e gene_by_sample_matrix.tsv -o corrected.tsv
The gene by sample matrix should look like this:
gene_id sample1 sample2 sample3 (...)
ENSG00000000005.5 1.87 2.66 0.74
ENSG00000000419.12 9.2 10.91 10.34
ENSG00000000457.13 7.35 8.26 7.16
(...)
The batch info file groups the samples by a characteristic such as tissue or tumor type:
id Batch
sample1 liver
sample2 liver
sample3 lung
(...)