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remove batch effect

I have a data set coming from two independent experiments. I see for some samples there are batch to batch response (final outcome) variation. Please guide me in- how to mitigate this batch effect in JMP.

Thanks

Analytics

Re: remove batch effect

The most obvious approach is to add a data column with the indication of the batch for each row (experimental run) and then include this data column as a covariate in your linear regression model. Be sure to define the modeling type of the batch column as nominal and do not include it in any interaction terms.

Re: remove batch effect

Mark

Can you elaborate on your last statement? Why would you not include the batch in any interaction terms? Absent interactions, aren't you permitting only the intercept of the model to vary by batch, whereas interactions also permit the slope coefficients to vary?

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