Batch correction best practices for DepMap omics expression data 25Q3

Q&A
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1

I’m using the 25Q3 OmicsExpressionTPMLogp1HumanProteinCodingGenes.csv dataset and had a question about applying batch correction. Currently, it seems like DepMap is looking for an alternative to ComBat to batch correct so pre batch corrected data isn’t provided. I was wondering if anyone has any guidance on performing batch correction ourselves for the newer DepMap releases? Otherwise, should I be using the existing ComBat batch-corrected expression data from 24Q4 even though there are negative values?

2

Hi,

OmicsExpressionTPMLogp1HumanProteinCodingGenes.csv, along with all the other expression files in 25Q3, are in fact not batch-corrected. While we continue to explore other batch correction methods, some annotation fields might potentially be helpful in approximating “batches” in your batch correction workflow, for example the “SequencingDate” and other columns in the OmicsProfiles table.

Thanks,

Simone

3

Do you have any specific suggestions of methods or processes to do the batch correction as of right now?