How to remove batch effect from TCGA and GTEx data I want to play some differentially expressed genes for gliomas cancer. I collected cancer tissue profiles from the TCGA database and normal tissue profiles from the GTEx database. I straightforward use ComBat from R package &quot;sva&quot;, and the result shows little differentially expressed genes (DEGs) were found. How can I remove batch effects correctly?
Thanks
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.