Dear List, I have a problem using the pairwise.comparison function in the simpleaffy package. > x.rma <- call.exprs(da, "rma") Background correcting Normalizing Calculating Expression > class(x.rma) [1] "ExpressionSet" attr(,"package") [1] "Biobase" > pData(x.rma) population KO KO het het > results <- pairwise.comparison(x.rma, "population", spots=da) Error in validObject(.Object) : invalid class "PairComp" object: invalid object for slot "pData" in class "PairComp": got class "factor", should be or extend class "data.frame" I already posted this error a while a go but without obtaining any answer... If anybody has experienced the same problem and managed to solved it, I would appreciate that he or she share his solution... Best, David --- > sessionInfo() R version 2.7.1 (2008-06-23) i386-apple-darwin9.4.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/C attached base packages: [1] splines tools stats graphics grDevices datasets utils methods base other attached packages: [1] mouse4302cdf_2.2.0 simpleaffy_2.16.0 gcrma_2.12.1 matchprobes_1.12.0 genefilter_1.20.0 [6] survival_2.34-1 affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.2.2 DBI_0.2-4 RSQLite_0.6-9 annotate_1.18.0 tcltk_2.7.1

Hi David -- David Ruau <david.ruau at="" rwth-aachen.de=""> writes: > Dear List, > > I have a problem using the pairwise.comparison function in the > simpleaffy package. > > x.rma <- call.exprs(da, "rma") > Background correcting > Normalizing > Calculating Expression > > class(x.rma) > [1] "ExpressionSet" > attr(,"package") > [1] "Biobase" > > pData(x.rma) > population > KO KO > het het There's no replication here, so no statistical conclusions can be made. but... > > results <- pairwise.comparison(x.rma, "population", spots=da) > Error in validObject(.Object) : > invalid class "PairComp" object: invalid object for slot "pData" in > class "PairComp": got class "factor", should be or extend class > "data.frame" get.fold.change.and.t.test subsets a data frame without drop=FALSE, so that when there is a single column (like in your x.rma) it produces a vector rather than data.frame. So a work-around would be to add a column to phenoData, e.g., lbl <- "Placeholder for simpleaffy workaround" phenoData(x.rma)[["pseudo", labelDescription=lbl]] <- NA Hope that helps, Martin > I already posted this error a while a go but without obtaining any > answer... > > If anybody has experienced the same problem and managed to solved it, > I would appreciate that he or she share his solution... > > Best, > David > --- > > sessionInfo() > R version 2.7.1 (2008-06-23) > i386-apple-darwin9.4.0 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/C > > attached base packages: > [1] splines tools stats graphics grDevices datasets utils > methods base > > other attached packages: > [1] mouse4302cdf_2.2.0 simpleaffy_2.16.0 gcrma_2.12.1 > matchprobes_1.12.0 genefilter_1.20.0 > [6] survival_2.34-1 affy_1.18.2 preprocessCore_1.2.1 > affyio_1.8.1 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.2.2 DBI_0.2-4 RSQLite_0.6-9 > annotate_1.18.0 tcltk_2.7.1 > > _______________________________________________ > 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

David, I'll take a look at this and get back to you... Crispin On 5/8/08 13:47, "David Ruau" <david.ruau at="" rwth-aachen.de=""> wrote: > Dear List, > > I have a problem using the pairwise.comparison function in the > simpleaffy package. >> x.rma <- call.exprs(da, "rma") > Background correcting > Normalizing > Calculating Expression >> class(x.rma) > [1] "ExpressionSet" > attr(,"package") > [1] "Biobase" >> pData(x.rma) > population > KO KO > het het >> results <- pairwise.comparison(x.rma, "population", spots=da) > Error in validObject(.Object) : > invalid class "PairComp" object: invalid object for slot "pData" in > class "PairComp": got class "factor", should be or extend class > "data.frame" > > I already posted this error a while a go but without obtaining any > answer... > > If anybody has experienced the same problem and managed to solved it, > I would appreciate that he or she share his solution... > > Best, > David > --- >> sessionInfo() > R version 2.7.1 (2008-06-23) > i386-apple-darwin9.4.0 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/C > > attached base packages: > [1] splines tools stats graphics grDevices datasets > utils methods base > > other attached packages: > [1] mouse4302cdf_2.2.0 simpleaffy_2.16.0 gcrma_2.12.1 > matchprobes_1.12.0 genefilter_1.20.0 > [6] survival_2.34-1 affy_1.18.2 preprocessCore_1.2.1 > affyio_1.8.1 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.2.2 DBI_0.2-4 RSQLite_0.6-9 > annotate_1.18.0 tcltk_2.7.1 > > _______________________________________________ > 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 -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}