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4.9 years ago
My experiment aims to test the interaction between heterologous genes in a double transgenic mouse model. Basically the interaction of viral genes with 3 different variants of a human gene. The gene expression data was obtained with Affymetrix microarrays, and present 2 unwanted (and strong) sources of variation, batch and sex, and 2 wanted sources with different levels.
Batch (1st, 2nd) unwanted,
Sex (male, female) unwanted,
Viral Transgenes (present, not present),
Human transgenes (not present, variant1, variant2, variant3).
My question is what would be the best way to adjust the data to account for batch and sex effects. I was thinking on applying 2 sequential ComBat adjustments. Does this make sense? Are there better forms? Thanks.
