[BioC] Questions about limma

[He, Yiwen (NIH/CIT)]

Hi, I have some questions about the data that the limma package can work on.
If I have some preprocessed/normalized data of log2 ratios from 2-color
arrays, but not the raw signal data, can I still use lmFit? A related
question is, can limma work on a subset of the data from an array? For
example, after normalization, I filter out some probes/spots. If I can
retrieve the M and A values of that subset, can I still use limma?

 

Bottom line, do I always have to start with raw data while using limma?

 

Also, are there any test data available in the package?

 

Thank you, Yiwen

 

 

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Yiwen He, Ph.D., M.P.H.

Analyst/Web Developer

Contractor, SRA International Inc.

Bioinformatics and Molecular Analysis Section

Center for Information Technology

National Institute of Health

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Bldg. 12A, Rm. 1018

12 South Dr., Bethesda, MD 20892

Email: heyiwen at mail.nih.gov
Phone: 301-402-4636

Fax: 301-402-2867

 


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