Produce quantile normalized expression values for use with BatchQC
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Josh • 0
@josh-16816
Last seen 1 hour ago
University of Chicago

I have RNAseq data produced from multiple separate experiments that I want to analyze together. I would like to use BatchQC to evaluate the need and effect of batch effect correction. My understanding is that BatchQC requires "quantile normalized expression values". I have not been able to figure out how to perform this type of normalization. Is there an R package I can use to generate quantile normalized expression values"?

Thanks!

BatchQC • 99 views
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Malcolm Cook ★ 1.5k
@malcolm-cook-6293
Last seen 28 days ago
United States

I've no experience with BatchQC but

library(preprocessCore)       #  implements normalize.quantiles