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cellgeni / batchbench

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Bulk RNA seq #21

Closed mdanb closed 3 years ago

mdanb commented 3 years ago

Do the batch correction methods in batchbench work for Bulk RNA seq (instead of single cell)?

rubenchazarra commented 3 years ago

Hi @mdanb, The overall method requires the input to be a SingleCellExperiment object. I believe you can generate a SCE object with bulk RNA-Seq data, although some of the batch correction methods included have been specifically developed for scRNA-seq data, and account for the particularities of this type of data. This is why the behaviour of these methods can be unpredictable with bulk RNA-seq data. Nonetheless, BatchBench also includes some batch-correction methods initially designed for microarray and bulkRNA-Seq data (Limma, ComBat), in which case the method could work if you pack your data into an SCE object.

mdanb commented 3 years ago

@rubenchazarra "BatchBench also includes some batch-correction methods initially designed for microarray and bulkRNA-Seq data" which ones?

rubenchazarra commented 3 years ago

@mdanb These are Limma and ComBat