## User: Constantin Ahlmann-Eltze

- Reputation:
**10**- Status:
- New User
- Location:
- Germany/Heidelberg/EMBL
- Website:
- https://github.com/con...
- Twitter:
- const_ae
- Last seen:
- 4 weeks, 1 day ago
- Joined:
- 4 months, 1 week ago
- Email:
- a**********@googlemail.com

#### Posts by Constantin Ahlmann-Eltze

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... Ah, okay. Thanks for the clarification :)
> I wanted to take the completed matrix, correct for the batch effect and then run a statistical test
If the batch effect that you mentioned, is the one in the column of the design matrix, the best way to handle it is to include it in the linear model. ...

written 4 weeks ago by
Constantin Ahlmann-Eltze •

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... Well, yes you can get the completed matrix using
predict(fit, type = "response")
The documenation for the predict function is here [https://const-ae.github.io/proDA/reference/predict-proDAFit-method.html][1]
**But**, I think you should not do that and then run another statistical test on the ...

written 4 weeks ago by
Constantin Ahlmann-Eltze •

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... Hi Haris,
the problem that you are describing is exactly for what I developed `proDA`.
To show how you can use the package, I will generate some synthetic data to show how to call `proDA` with the appropriate linear model. I assume that your design matrix dataframe is called `design_matrix`.
...

written 4 weeks ago by
Constantin Ahlmann-Eltze •

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