1
$\begingroup$

I have recently sequenced a bulk dataset. However one of my conditions has a lot of contamination from other cell types. I was thus thinking of using a publicly available single-cell dataset of my cell type of intereset, perform a pseudobulk reduction and integrate the pseudobulk dataset into my bulk RNA seq data.

Is this possible ? Or would there be way too much transcriptome variation and batch to batch differences ? Can I normalize for batch somehow?

Improve this question
$\endgroup$

1 Answer 1

Reset to default
1
$\begingroup$

No, you cannot. It is a basic principle of any experiment that you cannot add data from completely unrelated other experiments and expect any meaningful quantitative readout. There is a batch effect between the existing data and the newly-added public data, and since batch and experimental group is the same here you cannot correct for it. Don't do that.

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.