extract specific DEG from RNA-SEQ data with batch effect

Question

[ystokar]

I would like to extract data on a specific gene from a publicly available RNA-SEQ data-set (GSE57804). The original analysis was done with EDGR including a batch factor but from looking at the normalized data there's still a clear batch effect. What would be the best way to display the differential expression of a single gene of interest? I thought of using the normalized counts from HTSEQ and then normalize per batch and disply the relative expression. Any thoughts?

[ATpoint]

Remove the batch effect, e.g. limma::removeBatchEffect feeding the entire matrix of normalized counts on the log2 scale.