Hello,

I will refer to two posts (links below), whereby similar question had been asked in the past: "How to extract normalized counts with covariates in the design" and there was no direct way to get the desired output.

https://support.bioconductor.org/p/69992/, https://support.bioconductor.org/p/68123/

Later on it was suggested to use removeBatch (https://support.bioconductor.org/p/62954/)

I have used SVA to account for not only batch affects but also other possible hidden covariates. In the current manual: https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf

plotCount functions has parameter "returnData". Is this the correct parameter to be used to extract the "custom post-normalization counts" and save to a file?

Thanks

In DESeq2, normalized counts control for sequencing depth, or calculated biases if you use tximport. We don't have a method for producing normalized counts that removes things like SVA or RUV factors.

If this is for visualization purposes, I would recommend the approach in the vignette, of computing the vst and then using removeBatchEffect to remove any unwanted variation, such as batch or SVs.