[BioC] Webbioc error exprSet vs expressionSet

[Martin Morgan]

Hi Bala --

Your script didn't make it through the mail filter. I'm guessing that 
the objects that are causing the problem are 'serialized' -- saved to 
disk -- rather than newly created by your revised pipeline. Likely the 
solution in R is

 > as(oldObj, "ExpressionSet")

Current bioconductor packages shouldn't be making exprSet; if they are, 
then please let use know. Especially if they are in the devel branch, 
which has had a fairly thorough going-over.

Martin

Balasubramanian Ganesan wrote:
> Dear all
> I am  attaching the CGI scripts that we typically use for webbioc on a 
> shared computer.
> I finally had the guts to upgrade R in our machine after running 2.1 for 
> a really long time, as it still was facilitating analysis for naive users.
> I finished completely building R from source and installing all required 
> packages to run on our machine successfully.
> However we still are a little stuck.
> The preprocessing by the aff.cgi script works fine, and I can get 
> normalized data out of it.
> But when I try to run multtest using multtest.cgi, it brings up an error 
> on the web page called "Invalid object class".
> After fishing around for a while, I figured that it is because in 
> earlier versions the normalized data were stored in a session as an 
> "exprSet" object, but now it is stored as an "ExpressionSet" object, and 
> hence does not get recognized.
> How to resolve this issue?
> Any suggestions on what should be tweaked and how are welcome.
> 
> Balasubramanian Ganesan
> Research Assistant Professor
> Center for Integrated BioSystems
> Utah State University
> 4700 Old Main Hill
> Logan UT 84322
> balag at cc.usu.edu
> 
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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