[BioC] a bug in the function pamr.plotcen()

[Martin Morgan]

Hi Alex -- Thanks for the report and reproducible example; see the 
comment below...

On 06/06/2011 11:33 AM, Alogmail2 at aol.com wrote:
>
> Dear All,
>
> It looks like I found a bug in the function pamr.plotcen() of the  package
> pamr
> in this row:
>
> genenames<- data$genenames[fit$gene.subset]
>
> there is no such name in the output list of pamr.train(mydata)
>
>
> Thanks
>
> Alex
>
>
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>
>> set.seed(120)
>> x<- matrix(rnorm(1000*20),ncol=20)
>> y<- sample(c(1:4),size=20,replace=TRUE)
>> mydata<-  list(x=x,y=y)

Try

mydata <-  list(x=x,y=y, genenames=as.character(1:1000))

I arrived at this by looking at ?pamr.plotcen and knowing that the 
examples have to work for the package to be available for biocLite.

Martin

>> mytrain<-    pamr.train(mydata)
> 123456789101112131415161718192021222324252627282930>   mycv<-
> pamr.cv(mytrain, mydata)
> 1234Fold 1  :123456789101112131415161718192021222324252627282930
> Fold 2  :123456789101112131415161718192021222324252627282930
> Fold 3  :123456789101112131415161718192021222324252627282930
> Fold 4  :123456789101112131415161718192021222324252627282930
>>   pamr.plotcv(mycv)
>> pamr.plotcen(mytrain, mydata,threshold=1.6)
> Error  in text.default(rep(0, nd), seq(nd), label = g, cex = 0.4, adj = 0,
> :
> zero length 'labels'
>
>
>> names(mytrain)
> [1]  "y"                 "proby"             "yhat"
> [4]  "prob"              "centroids"         "centroid.overall"
> [7]  "sd"                "threshold"         "nonzero"
> [10]  "threshold.scale"   "se.scale"          "scale.sd"
> [13]  "call"              "hetero"            "norm.cent"
> [16]  "prior"             "offset"            "sign.contrast"
> [19]  "errors"            "gene.subset"      "sample.subset"
> [22]  "ngroup.survival"  "problem.type"
>
>
>
>
>
>
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform:  i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2]  LC_CTYPE=English_United States.1252
> [3]  LC_MONETARY=English_United States.1252
> [4]  LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines    tools     stats     graphics   grDevices utils     datasets
> [8] methods    base
>
> other attached packages:
> [1]  pamr_1.51       survival_2.36-5  cluster_1.13.3  xtable_1.5-6
> [5] Rmagpie_1.6.0    Biobase_2.10.0  RWeka_0.4-7
>
> loaded via a namespace (and not attached):
> [1]  class_7.3-3        e1071_1.5-25       grid_2.12.2       kernlab_0.9-12
>
> [5] rJava_0.8-8       RWekajars_3.7.3-1
>
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