DE Analysis on multiple batch data

[hkarakurt8742]

Hello and thank you for amazing tool.
I have a question about the data with multiple batches. I am using MNN (in Scater/Scran) and the correction method gives corrected space. It is not adviced to use corrected space values since they do not correspond to expression levels anymore (data has negative values).
Is it possible to use DESingle on data comes from different batches (or conditions)?

Thank you in advance.

[miaozhun]

Hi @hkarakurt8742,
Sorry to reply late. It is OK to use DESingle on data comes from different batches (or conditions), while the experiment design should be balanced among the groups compared.
For example, to compare cell group A with cell group B, it is OK when 20% cells of group A come from batch 1 and also 20% cells of group B come from batch 1, and so on...
And for the corrected space values, DEsingle will not accept negative values, so I'm afraid it will not work for the corrected space values.
I hope this will help you : )