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Question: Using Limma for analyzing proteomics data
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gravatar for cookm346
2.5 years ago by
cookm3460
cookm3460 wrote:

I have seen many researchers use (and instruct on how to use) Limma for analyzing genomics data. What are the changes that need to be made to the way Limma is used for analyzing Proteomics data?

 

Thank you so much.

ADD COMMENTlink modified 2.5 years ago by Laurent Gatto1.0k • written 2.5 years ago by cookm3460
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gravatar for Laurent Gatto
2.5 years ago by
Laurent Gatto1.0k
United Kingdom
Laurent Gatto1.0k wrote:

This will depend on what data you intend to use. If you have spectral counts, limma is not a good choice (see msmsTests instead). Otherwise, limma can be used as is for proteomics data. What you will need to do is to process/normalise your data, ... according to the mass spectrometry and quantitation you have used. But that's independent of limma, really.

 

ADD COMMENTlink written 2.5 years ago by Laurent Gatto1.0k
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