Batch effect removal (Combat)
Hi! I want to remove batch effect from a count data matrix (RNAseq experiment) using Combat function (sva package). I know that RemoveBatchEffect function (from Limma package) needs Log-transformed input, however Combat manual doesn't mention whether input data should be Log-transformed...
Thank you in advance!!
Combat manual: https://bioconductor.org/packages/release/bioc/manuals/sva/man/sva.pdf
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GSAENZDEPIP •
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The sva tutorial states one can extract the expression data from the expressionSet object:
The expression data can be obtained from the expression slot of the expression set.
edata = exprs(bladderEset)
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Thank you! I have just found the answer in the tutorial: "For sequencing data, which are often represented as counts, a more suitable model may involve the use of a moderated log function"