Error in R package "cancerclass" with function nvalidate
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svlachavas ▴ 830
@svlachavas-7225
Last seen 7 months ago
Germany/Heidelberg/German Cancer Resear…

Dear ALL,

i tried to implement the R package "cancerclass" with a microarray colon cancer dataset to evaluate and create possible predictors in order to classify cancer vs control samples, as described in the vignette. My pData(ExpressionSet) is the below:

 

pData(data.trusted.eset)
                                  condition            Meta_factor
7_Tesch.CEL               Normal               0
8_Tesch.CEL               Cancer               0
0687_04_Blauth.CEL        Normal            0
0687_04_Blauth_1.CEL      Cancer           0
0863_03_Schmidt.CEL       Normal           0
0863_03_Schmidt_1.CEL     Cancer          0
0948_04_Leiber.CEL        Normal             0
0948_04_Leiber_1.CEL      Cancer            0
1043_04_Nagel.CEL         Normal             0
1043_04_Nagel_1.CEL       Cancer           0
1103_03_Braun.CEL         Normal           1
1103_03_Braun_1.CEL       Cancer           1
1234_06_Floersch.CEL      Normal           0
1234_06_Floersch_1.CEL   Cancer          0
1235_06_Hey.CEL             Normal           0
1235_06_Hey_1.CEL         Cancer           0
1236_06_Liebich.CEL         Normal           1
1236_06_Liebich_1.CEL     Cancer           1
1410_03_Urbaniak.CEL       Normal           1
1410_03_Urbaniak_1.CEL    Cancer          1
1430_04_Patschke.CEL       Normal          0
1430_04_Patschke_1.CEL    Cancer          0
1518_03_Dege.CEL              Normal          0
1518_03_Dege_1.CEL          Cancer           0
1554_03_Gemmer.CEL         Normal           1
1554_03_Gemmer_1.CEL      Cancer          1

However, when i use the function 

gene.validation <- nvalidate(data.trusted.eset,class=pData(data.trusted.eset)[1], ngenes=c(5, 10, 20, 50, 100, 200), method="wilcoxon.test")

it gives me the following error:

WARNING: class is not defined for all samples!
Removing 26 samples from the data set.
WARNING: Data set contains missing genes!
Removing 7904 genes from the data set.
Error in .subset(x, j) : invalid subscript type 'list'
In addition: Warning message:
In is.na(pData(eset)[[class]]) :
  is.na() applied to non-(list or vector) of type 'NULL'

i also tried different inputs for argument "class", but nothing happens and the same error appears !!

Any help or suggestions ?

 

 

cancerclass bioconductor machinelearning classification • 1.4k views
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