[BioC] How to create expression data packages

Robert Gentleman rgentlem at fhcrc.org
Tue Jul 18 01:47:11 CEST 2006

  If you want to create a package, then some of the operations are 
detailed in Section 1 of the Writing R Extensions Manual (that came with 
R). In particular you might find the function package.skeleton helpful.
  Creating a package is a bit more work than just creating separate 
files you can pass around, but it is also a bit more useful, as you can 
create manual pages, and there is a simple way to version it (in case 
you update the data, or add data) etc.

  I would create each of the different data sets, as you have described 
below, but instead of giving them names like eset, you should give them 
names that are more meaningful and would help to identify the data.
  Then you can save these, (using save), copy the resulting objects into 
the data director/folder of your package. For each object you should 
create a manual page (prompt can help a bit), and put the resulting .Rd 
file into the man directory.

  Building, is done with R CMD build, checking with R CMD check (on 
Unix). On Windows you need to do a lot more work (as you will need to 
install most of the tools needed to build packages etc).

  best wishes

Srinivas Iyyer wrote:
> Dear group, 
>  I have 15 gene expression studies.  I have raw data
> for these (some are GEO datasets). 
> I could make esets for these datasets. 
> i want to create  expression data packages, so that my
> peers can also use these datasets for their analysis. 
> I have the following components for each dataset:
> 1.phenoData
> 2.expression data matrix
> 3. detailed annotations including clinical variables
> embeded into phenoData. 
> I could make an eset for these:
> eset <- new('exprSet',data = exp.mat, phenoData=pheno)
> from now on how can I go ahead and make expression
> data library. 
> Is there any step-by-step procedure to create a
> experimental data library. 
> could any one pls. help me.
> thanks
> srini
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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