[BioC] screeplot in package pcaMethods fails

[Yannick Wurm]

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
>
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