Is it possible to choose different normalization methods?

[bigomics]

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[premsubr in googlegroups 03.05.2021]

Is it possible to choose different normalization methods? TMM, etc....

[bigomics]

Not yet but there is already some initial work being done in the shiny/modules/normalizeCountsModule.R where the user can choose between normalization methods through the GUI at upload. There are still some considerations because internally, we use CPM+quantile for the limma and ttest based tests, where EdgeR and DEseq2 still use their own normalization methods. So if we allow to choose normalization, we need to skip the normalization in the EdgeR and DEseq2 calls.

[github-actions[bot]]

This issue is stale because it has been open for 60 days with no activity. It will close in 14 days.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.