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

[Brian D Ripley]

'Frankly, this is troubling' that you did not read the FAQ.  This is a 
contributed package (from BioC, I presume) and you should report your 
troubles to the maintainer or the BioC support lists.

Please do read the FAQ to find out why you have made work for people 
with better things to do.

On Thu, 22 Jan 2009, guy.tillinghast at rivhs.com wrote:

> 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.
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595