[BioC] about understanding contrast matrix

James W. MacDonald jmacdon at med.umich.edu
Tue Jul 4 15:17:23 CEST 2006

Hi Yanju,

yanju at liacs.nl wrote:
> Dear Bioconductors,
> In analyse of DNA microarray using LIMMA: for example you have a contrast
> matrix like follow:
> ---makeContrasts(B-A,C-B,levels=c("A","B","C"))
> then it is fitted to linear model and eBayes function is used to summarize
> the statistics.
> Finally log odds is used to rank the differential genes.
> I am wondering is the log odds rank the genes which express different
> between condition B and A (B-A), or C and B(C-B), or different in both
> conditions, or in either conditions? how to explain it?

The log odds rank the genes differently for each individual contrast. If 
you type topTable(<MArrayLM_object>, coef = 1), you will get the top 
genes in the first contrast, and if you type topTable(<MArrayLM_object>, 
coef = 2), you get the top genes in the second contrast.



> Expecting your reply!
> Regards,
> Yanju
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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