Trouble with multtest
0
0
Entering edit mode
dutzr14 • 0
@dutzr14-14175
Last seen 6.5 years ago

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?

mt.teststat multtest • 863 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 964 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6