How to remove batch effect from TCGA and GTEx data
This has been asked and answered here and Biostars. My take home message from many similar posts is &quot;not to bother with correcting batch effects when performing differential expression analysis but to include 'batch' as a covariate&quot;. The latter accounts for the batch effects.
EDIT: This does not really answer OP's question, as @swbarnes2 and @ATpoint pointed out, they have a completely confounded design and the linear regression model would not accept such a model matrix.