[BioC] affycoretools limma2annaffy fold change output question

[James W. MacDonald]

Hi Mark,

Kimpel, Mark William wrote:
> In the package affycoretools, how does the function limma2annaffy
> determine which fold change to output in the case of multiple contrasts?
> In topTable, one can specify the coefficient, but I don't see that this
> is the case with limma2annaffy.

In limma2annaffy, one of the arguments you supply is the contrasts 
matrix. This is used to extract the fold change, t-statistic, p-value, 
and expression values for the resulting HTML or text table.

The default is to output results for _all_ contrasts, so you don't 
explicitly specify the coefficient.

HTH,

Jim


> 
> 
> Thanks,
> 
> Mark W Kimpel
> Indiana University School of Medicine
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.