encountering difficulty asking R to manipulate the correct columns in Expression Set class (object 4). (PR#13464)

Full_Name: Guy W. Tillinghast
Version: 2.8.0
OS: Windows XP professional
Submission from: (NULL) (24.248.24.3)


I am encountering difficulty asking R to manipulate the correct columns in
Expression Set class (object 4).

I download the ALL data with:
library(golubEsets)
data(Golub_Merge)

Note, the data has the samples not in order.  This is not R's fault (at least
not that I can tell):

Golub_Merge$Samples

[1] 39 40 42 47 48 49 41 43 44 45 46 70 71 72 68 69 67 55 56 59 52 53 51 50 54
[26] 57 58 60 61 65 66 63 64 62  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16
[51] 17 18 19 20 21 22 23 24 25 26 27 34 35 36 37 38 28 29 30 31 32 33

I want a subset:

learning.set<-c(1,2,3,6,8,10,11,12,13,15,16,17,18,19,20,21,23,24,26,30,31,32,34,35,36,37,39,43,44,45,46,47,48,49,50,51,52,53,55,56,57,58,59,60,62,63,64,65,66,67,68,69,70,72)
learningEset<-Golub_Merge[,learning.set]
learningEset$Samples

[1] 39 40 42 49 43 45 46 70 71 68 69 67 55 56 59 52 51 50 57 65 66 63 62  1  2
[26]  3  5  9 10 11 12 13 14 15 16 17 18 19 21 22 23 24 25 26 34 35 36 37 38 28
[51] 29 30 31 33
Note what happened: 
1)	the order is difference than learning.set
2)	samples have been switched: example: sample 72 out, sample 71 in. 

Okay, I troubleshoot: maybe it matters what order I request samples:

learning.set<-c(39,47,48,49,43,44,45,46,70,72,68,69,67,55,56,59,52,53,51,50,57,58,60,65,66,63,64,62,1,2,3,6,8,10,11,12,13,15,16,17,18,19,20,21,23,24,26,34,35,36,37,30,31,32)
learningEset<-Golub_Merge[,learning.set]
learningEset$Samples

[1]  5 13 14 15  9 10 11 12 31 33 29 30 28 21 22 25 18 19 17 16 23 24 26 37 38
[26] 35 36 34 39 40 42 49 43 45 46 70 71 68 69 67 55 56 59 52 51 50 57 62  1  2
[51]  3 65 66 63
Frankly, this is troubling that R did not do what it was told.