[BioC] affycoretools limma2annaffy fold change output question

James W. MacDonald jmacdon at med.umich.edu
Wed Apr 19 17:03:52 CEST 2006

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.



> 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.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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

More information about the Bioconductor mailing list