Yes, I guess you're expected to use the following instead pcaMethods::plotR2 On Dec 12, 2008, at 0:41 , Wolfgang Huber wrote: > > Hi Yury, > > thank you. As far as I can tell, no "screeplot" method is defined > by the pcaMethods package, so you would be falling back on > stats:::screeplot.default, whose implementation indeed asks for x > $sdev and probably is what throws the error that you report > (remember next time to add the output of "traceback()" to your > error message). > > Perhaps the pcaMethods package documentation could be clarified > regarding the existence and/or usage of a "screeplot" method. > (Typing "class ? pcaRes" currently tells you that such a method > exists.) > > Best wishes > Wolfgang > > ---------------------------------------------------- > Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber > > > Yury Bukhman ha scritto: >> Hi, I have created a pcaRes object using pcaMethods. slplot >> works OK, but screeplot fails with this error: >> R> screeplot(kubo1.pca) >> Error in x$sdev : $ operator not defined for this S4 class >> More info below. >> R> class(kubo1.pca) >> [1] "pcaRes" >> attr(,"package") >> [1] "pcaMethods" >> R> print(kubo1.pca) >> svd calculated PCA >> Importance of component(s): >> PC1 PC2 PC3 PC4 >> R2 0.4585 0.2713 0.1381 0.04216 >> Cumulative R2 0.4585 0.7299 0.8680 0.91014 >> 11405 Variables >> 12 Samples >> 0 NA's >> 4 Calculated component(s) >> Data was mean centered before running PCA Scores structure: >> [1] 12 4 >> Loadings structure: >> [1] 11405 4 >> R> sessionInfo() >> R version 2.8.0 (2008-10-20) x86_64-redhat-linux-gnu locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8; >> LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8; >> LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; >> LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8; >> LC_TELEPHONE=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8; >> LC_IDENTIFICATION=en_US.UTF-8 >> attached base packages: >> [1] splines tools stats graphics grDevices utils >> datasets [8] methods base other attached packages: >> [1] simpleaffy_2.16.1 genefilter_1.20.1 >> survival_2.34-1 [4] pcaMethods_1.18.0 pls_2.1-0 >> MASS_7.2-44 [7] affyPLM_1.16.0 gcrma_2.12.1 >> matchprobes_1.14.0 [10] affy_1.18.2 preprocessCore_1.2.1 >> affyio_1.8.1 [13] Biobase_2.0.1 rkward_0.4.9 >> loaded via a namespace (and not attached): >> [1] annotate_1.18.0 AnnotationDbi_1.4.2 DBI_0.2-4 [4] >> grid_2.8.0 lattice_0.17-15 latticeExtra_0.5-4 [7] >> RSQLite_0.7-0 Thanks. >> Yury > > _______________________________________________ > 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