[BioC] Finding Out the Fold Changes

[James MacDonald]

>From your email, it looks to me like you are trying to work through the
vignette for genefilter. If so, then wh2 in this case is a vector of
TRUEs and FALSEs, depending on the filter you applied to your data. If
you want the list of genes that pass the filter, you are going to have
to do something like:

goodgenes <- exprs(eset)[wh2,] # this will extract rows of your data
matrix where wh2 = TRUE

Then to output to a file, you cannot use write.exprs, because you no
longer have an exprSet, but a matrix. In this case you have to use
write.table:

write.table(goodgenes, file="My list of good genes.txt", sep="\t", etc
etc)

AFAIK, there is no listing of methods for all packages, but those
packages that use S4 methods usually have a listing of accessor
functions for the objects in the package (e.g., for exprSets,
AffyBatches, etc). Your best bet is to read all of the help files and
vignettes for the packages you are working with. It takes time, but
familiarity with 'how R works' only comes through time and effort.

HTH,

Jim



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

>>> "Sachin Mathur" <smathur at kumc.edu> 10/27/03 01:28PM >>>
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.

thanks
sachin.


>>> "James MacDonald" <jmacdon at med.umich.edu> 10/27/03 08:57AM >>>
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

HTH,

Jim



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

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

Hello,

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

thanks
sachin.

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