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VCCRI / CIDR

Clustering through Imputation and Dimensionality Reduction
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Input as batch effect corrected expression matrix #3

Open SharonWang opened 7 years ago

SharonWang commented 7 years ago

I am wondering if there is a way to use batch effect corrected expression matrix as input rather than raw counts?

paulyLin commented 7 years ago

Hi Sharon,

Yes, there is a way. After creating an scData class object using scDataConstructor, you can overwrite the default normalised data attribute nData with anything you like; for instance you can replace it with the batch effect corrected expression matrix.

Hope that it helps.

Regards, Paul

SharonWang commented 7 years ago

Dear Paul,

Thank you very much for your help! It worked very well.

best regards,

Sharon

From: paulyLin notifications@github.com Sent: 19 April 2017 14:19 To: VCCRI/CIDR Cc: SharonWang; Author Subject: Re: [VCCRI/CIDR] Input as batch effect corrected expression matrix (#3)

Hi Sharon,

Yes, there is a way. After creating an scData class object using scDataConstructor, you can overwrite the default normalised data attribute nData with anything you like; for instance you can replace it with the batch effect corrected expression matrix.

Hope that it helps.

Regards, Paul

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