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zhangyuqing / ComBat-seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data
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Genes reduced after ComBat-seq #1

Closed SL1993 closed 4 years ago

SL1993 commented 4 years ago

Hi, I have been using ComBat-seq for batch adjustment in a TCGA RNA-seq counts dataset. Before , there were 37,000 genes in that dataset. Somehow only 25,000s remained after adjustment. Was there any filtering conducted by ComBat-seq quietly? Or was it expected because of negative binomial regression which was applied in the function? Thanks.

SL1993 commented 4 years ago

Sorry for my ignorance. I have noticed the gene deleting command in your script. Seems ComBat-seq does conducting filtering by design.