Suresh, You should not cross-post questions to both BioC and R-help. This is considered bad form, and will not increase your chances of getting a helpful response (but will increase your chances of getting an abrupt rejoinder). This is clearly a BioC question. I haven't seen this particular error, so I am not sure of the exact cause. However, it appears that the BioC core are adding some new S4 objects to Bioconductor, and your version of affy is somehow out of synch with another required package (probably Biobase). I checked the current version of affy devel, and it is still out of synch with Biobase because there is a new object called an exprMatrix in Biobase that hasn't made it to the current devel version of affy. Any new AffyBatch will fail because the se.exprs and exprs slots are supposed to be class exprMatrix but are class matrix instead. All this aside, there are two things you can do. First, update your bioconductor packages to the newest devel version and then download and build the affy tarball from the cvs page. If you don't know how to do this, then you can simply wait a day or two for the new affy build to appear on bioconductor. Probably affy 1.3.26 is what you will need. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Suresh Kumar Karanam" <sureshkaran@hotmail.com> 10/27/03 05:33PM >>> Hi, I was using the affy package in R for sometime. I reinstalled the R environment lately due to some other issues and now I get errors when I use the function ReadAffy. The error is reproduced here: Error in validityMethod(object): No slot of name "phenoLabels" for this object of class "phenoData" I don't know what's wrong. Any help appreciated. thanks, suresh _________________________________________________________________ Cheer a special someone with a fun Halloween eCard from American Greetings! Go to http://www.msn.americangreetings.com/index_msn.pd?source=msne134 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Since we never did get an answer to Suresh's question: the error message indicates that you have an instance of a particular class (in this case phenoData) and it is incomplete. The validity checking function noticed this and signals an error. class?phenoData (the pattern is general, class?nameofclasshere) will get you the manual page that describes the class. Every object (or instance) from that class must have all slots. From the man page (sorry about the spelling....) Slots: 'pData': Object of class "data.frame". The data. 'varLabels': Object of class "list". Obtional long labels for the different variables. So this is documented incorrectly (and will make it in that form into the next release), the varLabels should not be optional. How can you fix this: you can add a list to your object that fails the validity test. Suppose, for example that the object in question is named myobject and that names(myobject@pData) returns A, B and C. This means you have three variables that need documenting, you could do something like: myobject@varLabels <- list(A="Variable A", B="Variable B", C="Variable C") Now, of course it would be better to put more descriptive labels here, like what units etc these are measured in. Then validObject(myobject) should return TRUE. Now, you might wonder how did this happen? Well, lots of ways. Basically validity checking has only recently been turned on (it slows things down a fair bit), and it exposed bugs in code, there are undoubtedly more, but we will get there and having validity checking turned on helps us get there more quickly, Robert On Tue, Oct 28, 2003 at 09:23:33AM -0500, James MacDonald wrote: > Suresh, > > You should not cross-post questions to both BioC and R-help. This is > considered bad form, and will not increase your chances of getting a > helpful response (but will increase your chances of getting an abrupt > rejoinder). This is clearly a BioC question. > > I haven't seen this particular error, so I am not sure of the exact > cause. However, it appears that the BioC core are adding some new S4 > objects to Bioconductor, and your version of affy is somehow out of > synch with another required package (probably Biobase). > > I checked the current version of affy devel, and it is still out of > synch with Biobase because there is a new object called an exprMatrix in > Biobase that hasn't made it to the current devel version of affy. Any > new AffyBatch will fail because the se.exprs and exprs slots are > supposed to be class exprMatrix but are class matrix instead. > > All this aside, there are two things you can do. First, update your > bioconductor packages to the newest devel version and then download and > build the affy tarball from the cvs page. If you don't know how to do > this, then you can simply wait a day or two for the new affy build to > appear on bioconductor. Probably affy 1.3.26 is what you will need. > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> "Suresh Kumar Karanam" <sureshkaran@hotmail.com> 10/27/03 05:33PM > >>> > Hi, > I was using the affy package in R for sometime. I reinstalled the R > environment lately due to some other issues and now I get errors when I > use > the function ReadAffy. The error is reproduced here: > > Error in validityMethod(object): No slot of name "phenoLabels" for this > > object of class "phenoData" > > I don't know what's wrong. Any help appreciated. > thanks, > suresh > > _________________________________________________________________ > Cheer a special someone with a fun Halloween eCard from American > Greetings! > Go to http://www.msn.americangreetings.com/index_msn.pd?source=msne134 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+