Question: Webbioc error exprSet vs expressionSet
0
gravatar for Balasubramanian Ganesan
11.1 years ago by
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
ADD COMMENTlink modified 11.1 years ago • written 11.1 years ago by Balasubramanian Ganesan70
Answer: Webbioc error exprSet vs expressionSet
0
gravatar for Martin Morgan
11.1 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k 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
ADD COMMENTlink written 11.1 years ago by Martin Morgan ♦♦ 23k
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
ADD REPLYlink written 11.1 years ago by Balasubramanian Ganesan70
Answer: Webbioc error exprSet vs expressionSet
0
gravatar for Balasubramanian Ganesan
11.1 years ago by
Forgot to add. We are using R on Mac OS X Panther 10.3.9. One thought did occur to me - is it a Perl parser issue, as at the earlier steps, it is Perl which is involved in reading in the files? In which case, I did update RSPerl as well, but is this issue already resolved in RSPerl? On Apr 3, 2008, at 1:24 PM, 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 Balasubramanian Ganesan Research Assistant Professor Center for Integrated BioSystems Utah State University 4700 Old Main Hill Logan UT 84322 balag at cc.usu.edu
ADD COMMENTlink written 11.1 years ago by Balasubramanian Ganesan70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 280 users visited in the last hour