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DavisLaboratory / GeoMXAnalysisWorkflow

GeoMX analysis workflow
https://davislaboratory.github.io/GeoMXAnalysisWorkflow/
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Batch correction after TMM or non-normalized #6

Open yeswzc opened 1 year ago

yeswzc commented 1 year ago

Hi, in the workflow, you did normalization and get an object of spe_tmm from spe. Batch correction was later performed by spe not spe_tmm. Should I use spe to perform batch correction or spe_tmm?

Thanks

ningbioinfo commented 11 months ago

Hi, sorry for the late reply. But either way, it shouldn't affect the DE results much.