I am working with SNP array data and want to know how to correct batch effect, but many sources are about expression data. I am confused if Combat can be used on SNP array intensity data? If no, What package can do this?
Thanks in advance!
You mean you are trying to perform a GWAS study? e.g. perform regression on SNPs against a phenotype of interest? If that is the case, one way is to include the batch as a covariate in your analysis
No, I'm trying to use SNP array signal intensity data to estimate CNV type. Do you know how to correct batch effect for this data?
It depends on what is your ultimate goal (?). You could try to 'regress out' the observed effect over the probe intensities.
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