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Question: screeplot in package pcaMethods fails
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gravatar for Yury Bukhman
8.9 years ago by
Yury Bukhman10
Yury Bukhman10 wrote:
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
ADD COMMENTlink modified 8.9 years ago by Wolfgang Huber13k • written 8.9 years ago by Yury Bukhman10
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gravatar for Wolfgang Huber
8.9 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k 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
ADD COMMENTlink written 8.9 years ago by Wolfgang Huber13k
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
ADD REPLYlink written 8.9 years ago by Yannick Wurm220
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