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lmweber / diffcyt

R package for differential discovery analyses in high-dimensional cytometry data
MIT License
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CONTRAST DOUBT #15

Closed DomenicoSkyWalker89 closed 4 years ago

DomenicoSkyWalker89 commented 4 years ago

Hi @lmweber , thanks for the pakage and the support. I have a doubt regarding the contrast. I have two groups (CTRL and TREATED), using contrast (0,1) all p value show no significance but changing contrast (1,0) five population are different. I also find this last result using the contrast (-1,1). This make me confused.

Thanks, Domenico

markrobinsonuzh commented 4 years ago

@DomenicoSkyWalker89

You need to give a complete description. I wouldn't expect contrasts (0,1) and (1,0) to give similar results, because they are testing different parameters of the model. And, (-1, 1) is again testing something different. I would suggest having a read through perhaps the limma or edgeR user's guide (e.g., the case studies) to get a handle on how to pair design matrices and contrasts. Or, a general resource on linear modeling.

If you ask a question here, please give full details, e.g., what is the design matrix?

DomenicoSkyWalker89 commented 4 years ago

Sorry for the few information. I followed the CATALYST workflow using flow cytometry data.

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