Hi all,

I was wondering if I could get some help with a copy number variation analysis I am running. I am currently using ChAMP to run the analysis and I am fairly new at it. Is there a way to run a normalization and batch effect correction on the intensity values to clean up the data before I run champ.CNA on these values? I have been using champ.runCombat() and champ.norm() but both work with the beta values not intensity values.

Any help would be much appreciated and thanks in advance!

From https://www.bioconductor.org/packages/devel/bioc/vignettes/ChAMP/inst/doc/ChAMP.html @ 6.11:

Note that different from old version of ChAMP. No batch correction would be run automatically on intensity data, if you want to correct batch effect on intensity data, please use champ.runCombat(), the usage for intensity data is exactly the same for beta or M matrix, the only difference is you need to replace the beta value with myLoad$intensity and set logitTrans=FALSE.