Limma help (creating design matrix)
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d808bc07 • 0
@d808bc07
Last seen 4 weeks ago

Hi, I'm trying to use limma to get a list of differentially expressed genes between subtypes (GCB and ABC) of B-cell lymphoma. I have a dataset from an Affymetrix array with gene expression reads for 271 samples. 71 of which were classified as ABC, 144 as GCB and 56 were unclassified.

I've managed to read my CEL files and perform normalisation on the gene expression data:

norm.batch = rma(batch)
dat = exprs(norm.batch)


But I'm just not sure where to start with creating a design matrix for the limma analysis

limma • 112 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

There's no need to do the second line in your example. The limma package is quite happy to accept an ExpressionSet as input, so you don't need a matrix. In addition, you could hypothetically include gene information in your ExpressionSet which will then be included in your output.

Anyway, have you read the limma User's Guide? Section 9.3 seems to be exactly what you are after.