[BioC] Webbioc error exprSet vs expressionSet

[Balasubramanian Ganesan]

Hi Martin
Thanks for the note.
No, it is NOT bioconductor making exprSet objects. But our old  
version (R2.1) is configured to create and re-read only exprSet  
objects, and cannot read ExpressionSet objects as well.
I just added another post, may be look at that. I think it has to do  
with Perl/RSPerl.
Now I have saved the cgi scripts as text. Hopefully they do come  
through.

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On Apr 3, 2008, at 1:41 PM, Martin Morgan wrote:
> 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
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793

Balasubramanian Ganesan
Research Assistant Professor
Center for Integrated BioSystems
Utah State University
4700 Old Main Hill
Logan UT 84322
balag at cc.usu.edu