Entering edit mode
Yury Bukhman
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20
@yury-bukhman-3186
Last seen 7.9 years ago
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