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Bioconductor/sva combat batch correction.
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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
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