Batch effect for SNP array
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20 months ago
Taylor95 ▴ 10

Hey all, 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!

SNP batch effect combat sva • 502 views
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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

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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?

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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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