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Question: Trouble with multtest
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gravatar for dutzr14
5 weeks ago by
dutzr140
dutzr140 wrote:

I am trying to select the top 50 genes with the largest t statistic using

library(golubEsets)
data("Golub_Merge")

I am trying to use the mt.teststat command to get the t statistics and keep getting an error message 

Error in as.vector(data) : 
  no method for coercing this S4 class to a vector.

I thought I created a vector with 1's for ALL and 0's for AML

Golub_Merge.1<-Golub_Merge[,order(Golub_Merge$ALL.AML)]

> Golub_Merge.1$ALL.AML
 [1] ALL ALL ALL ALL ALL ALL ALL ALL ALL
[10] ALL ALL ALL ALL ALL ALL ALL ALL ALL
[19] ALL ALL ALL ALL ALL ALL ALL ALL ALL
[28] ALL ALL ALL ALL ALL ALL ALL ALL ALL
[37] ALL ALL ALL ALL ALL ALL ALL ALL ALL
[46] ALL ALL AML AML AML AML AML AML AML
[55] AML AML AML AML AML AML AML AML AML
[64] AML AML AML AML AML AML AML AML AML
Levels: ALL AML

class<-c(rep(1, times=47), (rep(0, times=25)))

> class
 [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[20] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[39] 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
[58] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

What is supposed to go in the class label part?

What am I doing wrong?

ADD COMMENTlink written 5 weeks ago by dutzr140

You showed us the error, but not the code that produced it. Could you show the rest of the code?

ADD REPLYlink written 5 weeks ago by Sean Davis21k
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