[BioC] I have trouble using the data from the AnnBuilder Vignette

James W. MacDonald jmacdon at med.umich.edu
Thu Nov 18 22:23:01 CET 2004

Richard Friedman wrote:
> Dear Jim, Robert, John, and Everybody,
>     Thanks for all of the help. I have apparently, using Jim's
> strategy, obtained the data on the test case.  However, I have had
> difficulty putting the data into a form I can use. I want
> to put all of the data in an Excel speadsheet with each gene
> a row and each data for each gene a column. I have tried
> reading in the library with (library"myPkg") but it doesn't acknowledge
> myPkg's existence.  There is a temporary folder written with the data
> in RDA and XML files, but I have not been able to read them in.

ABPkgBuilder does only what the name implies; it makes a package. You 
have to then install the package using R CMD INSTALL (from a command 
prompt) if you then want to be able to do library(myPkg). To go from an 
installed package to an Excel file may take a bit of work, considering 
that you will have several environments containing all your annotation data.

>     I would greatly appreciate any suggestions.
> Thanks and best wishes,
> Rich

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

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