[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.
HTH,
Jim
>
> 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
734-647-5623
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