Question: affycoretools limma2annaffy fold change output question
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gravatar for Kimpel, Mark W
13.6 years ago by
Kimpel, Mark W890 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. Thanks, Mark W Kimpel Indiana University School of Medicine
affycoretools • 378 views
ADD COMMENTlink modified 13.6 years ago by James W. MacDonald52k • written 13.6 years ago by Kimpel, Mark W890
Answer: affycoretools limma2annaffy fold change output question
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gravatar for James W. MacDonald
13.6 years ago by
United States
James W. MacDonald52k wrote:
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.
ADD COMMENTlink written 13.6 years ago by James W. MacDonald52k
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