[BioC] number of variable in svm plot

nofe [guest] guest at bioconductor.org
Tue Jun 18 01:50:34 CEST 2013

hi all,

the data set i have consists of

x which is a matrix of 39 cancer patients [rows] and 2000 gene names [colmns]. each cell is the value of the gene for a particular patient. there are two types of cancer people  representedas factor y.

here is the code:


#load database

 db <- read.csv(file="databases\\colon-cancer\\colon-cancer.csv",head=FALSE,sep=",") 

x = as.matrix(db[,1:(ncol(db)-1)])
  y = as.factor(db[,ncol(db)])

  svmModel = svm(x, y, cost = 10, cachesize=500,  scale=F,
  type="C-classification", kernel="linear" )

my question is :to plot the svm model i need to plot 2 vaiables as y axis and x axis....but according to the nature of my dataset i have about 2000 variables?? does that mean i have to plot only two?? or is there a way to plot all of the 2000 and beable to show how the svm model classify the dataset. 

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=Arabic_Saudi Arabia.1256  LC_CTYPE=Arabic_Saudi Arabia.1256   
[3] LC_MONETARY=Arabic_Saudi Arabia.1256 LC_NUMERIC=C                        
[5] LC_TIME=Arabic_Saudi Arabia.1256    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] e1071_1.6-1          class_7.3-7          genefilter_1.42.0   
[4] ALL_1.4.14           Biobase_2.20.0       BiocGenerics_0.6.0  
[7] BiocInstaller_1.10.2

loaded via a namespace (and not attached):
 [1] annotate_1.38.0      AnnotationDbi_1.22.5 DBI_0.2-7           
 [4] IRanges_1.18.1       RSQLite_0.11.3       splines_3.0.1       
 [7] stats4_3.0.1         survival_2.37-4      tools_3.0.1         
[10] XML_3.96-1.1         xtable_1.7-1        

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