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Batch effects : ComBat or removebatcheffects (limma package)
Reading from many sources about how to correct for known batch effects present in a data expression compendium, I am now willing to understand which kind of batch effect correction method to apply
Negative values after Limmas batch effect correction
Limma assumes that both types of batch effects are additive and therefore independent Writing limma::removeBatchEffect(x = scores, batch = cancer_type, batch2 = study implies that there is no relation between the cancer type and the study dataset
Limma Batch Correction — adjust_limma • Giotto
svkey (optional) Up to two columns of information from a Giotto object with information indicating batches to remove the effects of svkey (optional) Columns of information from a Giotto object with information indicating covariates to regress out