[BioC] plotHist and plotDeg error

[James W. MacDonald]

How exactly did you re-install BioC? I ask because you have a mixture of 
BioC2.0 and BioC2.1, which is likely causing at least some of the problems.

Also, what exactly is celData?

Best,

Jim



Jason Pear wrote:
> Hi Dear BioC,
>  
> The plotHist and plotDeg worked well before, however, they gave me some error messages today.  I reinstall the R-2.6.1 and BioConductor and the errors stay the same.
>  
> Any suggestions?
>  
> Many thanks,
>  
> Jason
>  
> # ----------------------
>> plotDeg(celData)
> Error in UseMethod("as.double") : no applicable method for "as.double"
> In addition: Warning message:
> ':::' is deprecated.
> 'methods' is deprecated.
> 'seemsS4Object' is deprecated.
> Use 'isS4' instead.
> See help("Deprecated") 
>  
>> plotHist(celData)
> Error in checkSlotAssignment(object, name, value) : 
>   ".Data" is not a slot in class "matrix"
> In addition: Warning message:
> In par(op) : calling par(new=) with no plot
>  
>> sessionInfo()
> R version 2.6.1 (2007-11-26) 
> i386-pc-mingw32 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets  methods   base     
> other attached packages:
>  [1] hgu133plus2cdf_1.16.0 affycoretools_1.10.2  annaffy_1.10.1        gcrma_2.10.0         
>  [5] matchprobes_1.10.0    biomaRt_1.10.1        RCurl_0.8-0           XML_1.7-1            
>  [9] GOstats_2.2.6         Category_2.2.3        Matrix_0.99875-1      lattice_0.17-2       
> [13] genefilter_1.16.0     survival_2.34         KEGG_1.16.1           RBGL_1.12.0          
> [17] annotate_1.16.1       xtable_1.5-2          AnnotationDbi_1.0.6   RSQLite_0.6-4        
> [21] DBI_0.2-4             GO_1.16.0             graph_1.14.2          limma_2.12.0         
> [25] affy_1.16.0           preprocessCore_1.0.0  affyio_1.6.1          Biobase_1.16.1       
> loaded via a namespace (and not attached):
> [1] cluster_1.11.9 grid_2.6.1  
>  
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623