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. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: affycgi.txt Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080403/ 4dd2ca65/attachment.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: multtestcgi.txt Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080403/ 4dd2ca65/attachment-0001.txt -------------- next part -------------- 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 >> --------------------------------------------------------------------- >> --- >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor > > > -- > 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