I have a question about the presence of Batch effect in CCLE expression Affymetrix and RNASeq data.
What is the question?
Is there any batch effect in CCLE Affymetrix expression data? If yes, how to know batch IDs? Also, which package is recommended to remove batch effect- NOISeq or Combat?
The expression data that the DepMap project is generating is from RNA sequencing. The Affymetrix data you’re referring to sounds like it is part of the original CCLE expression dataset. In which case, I suspect the best contact for that question would likely be the authors of the paper the data was published with.