[BioC] Finding Out the Fold Changes

Sachin Mathur smathur at kumc.edu
Mon Oct 27 19:28:39 MET 2003

Thanks for the reply.

RMA is a wonderful package, which allows the analysis in various ways.
The difficuly i'm facing is trying to figure out what  methods apply to
a particular package.

 For example, when using genefilter to find out differentially
expressed genes, its difficult for me to output the entire list in a
text or excel file. When I try to use "
write.exprs(wh2,file="differ.txt")", it gives me an error saying that
write.exprs is not applicable to Genefilter Package. Is there
documentation which provides the methods and classes which a package
provides? the vignettes seem to lack this information. 
It would be very useful to have a comprehensive listing of packages
with their methods.


>>> "James MacDonald" <jmacdon at med.umich.edu> 10/27/03 08:57AM >>>
The expression values from RMA are log2 transformed, so to calculate
log ratio you simply subtract one from the other.

log2(x) - log2(y) = log2(x/y)

Note here the the log ratio gives you the fold change directly. A log
ratio of 1 = 2-fold up regulated and a log ratio of -1 = 2-fold down
regulated (when comparing x vs y).

There is no command per se, you simply have to do it yourself. The
expression values are held in a matrix in an exprSet and can be
using the exprs accessor. So if you wanted the log ratio of your first
sample as compared to the second, you would do something like

LR <- exprs(eset)[,1] - exprs(eset)[,2] # where eset is the name of
your exprSet



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

>>> "Sachin Mathur" <smathur at kumc.edu> 10/26/03 05:37PM >>>


I'm new to RMA. Can anyone tell me which command to use for finding
the fold changes for a given set of genes. 


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