[BioC] Finding Out the Fold Changes

James MacDonald jmacdon at med.umich.edu
Mon Oct 27 15:57:39 MET 2003

The expression values from RMA are log2 transformed, so to calculate the
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 accessed
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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