[BioC] screeplot in package pcaMethods fails

[Yury Bukhman]

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