[R] Matrix resampling (bootstraps)

[James MacDonald]

Putting aside the issue of whether you should be using boot() or not,
you can resample your matrix by doing something like this.

> a <- matrix(1:10, nrow=10, ncol=10, byrow=TRUE)
> a
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    1    2    3    4    5    6    7    8    9    10
 [2,]    1    2    3    4    5    6    7    8    9    10
 [3,]    1    2    3    4    5    6    7    8    9    10
 [4,]    1    2    3    4    5    6    7    8    9    10
 [5,]    1    2    3    4    5    6    7    8    9    10
 [6,]    1    2    3    4    5    6    7    8    9    10
 [7,]    1    2    3    4    5    6    7    8    9    10
 [8,]    1    2    3    4    5    6    7    8    9    10
 [9,]    1    2    3    4    5    6    7    8    9    10
[10,]    1    2    3    4    5    6    7    8    9    10
> b <- sample(1:10, replace=TRUE)
> b
 [1]  2 10  7 10  5  1  4  5  9  5
> d <- a[,b]
> d
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    2   10    7   10    5    1    4    5    9     5
 [2,]    2   10    7   10    5    1    4    5    9     5
 [3,]    2   10    7   10    5    1    4    5    9     5
 [4,]    2   10    7   10    5    1    4    5    9     5
 [5,]    2   10    7   10    5    1    4    5    9     5
 [6,]    2   10    7   10    5    1    4    5    9     5
 [7,]    2   10    7   10    5    1    4    5    9     5
 [8,]    2   10    7   10    5    1    4    5    9     5
 [9,]    2   10    7   10    5    1    4    5    9     5
[10,]    2   10    7   10    5    1    4    5    9     5

HTH,

Jim


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Hector L. Ayala-del-Rio" <ayalahec at msu.edu> 09/09/03 12:11AM >>>
Dear all,
    I am trying to generate bootstrap replicate matrixes (rows=samples,

column=species, sampling with replacement) from a matrix dataset, but I
do 
not know how to do it in R.  I have tried boot() and bootstrap(), but
they 
require an statistic, which in my case is cluster analysis (generating

bootstrap values for a cluster analysis is a topic that has been
mentioned 
previously in this list).  I have been trying to use sample() and
matrix() 
to generate the replicate matrix but they seem to generate a single
vector 
rather than the entire matrix.  What I want is to resample the entire 
matrix, but by resampling different columns (species).  In that way,
the 
bootstrap values will give me an idea of how similar the samples are. 
Any 
ideas will be very very helpful.  An example of that data matrix is
below.

Thanks

Hector

   X36C X40C X58C X60C X62C X66C X77C X92C X95C X96C X107C X109C X116C
26Y        0    0    0   59  919  351  128    0  104  214     0     0  
  0
C-0        0    0    0  368 1343 1826  211    0  253  352     0     0  
  0
C-50       0    0    0  211 1032 1701   50    0   54   56     0     0  
  0
C-90      64    0   65  260  769  876    0    0   87    0     0    91  
 96
C-127-1    0    0  127  149  364 3990    0    0    0    0     0     0  
  0
C-164      0    0    0   68  179 2373    0    0  105    0     0     0  
  0
C-198      0    0    0   89  327 1458  314    0  209  298     0     0  
  0
C-226      0    0    0    0  206  858    0    0  363  304     0     0  
  0
C-268      0    0    0   75  270  629    0    0  107    0     0     0  
  0
C-294-C   54    0    0  112  379  753    0  220  823  325     0     0  
  0
C-310      0    0    0    0  116  305    0  396 1049  355     0     0  
  0
C-357-2   96    0    0  445  201  405    0  114 2265    0   178    99  
125
C-375     90    0   56  231  385  817    0  211 2776    0    57    79  
106
C-399    110    0   50  563 1060 1244    0  414 2933    0    54   107  
123
C-414     64    0    0  197  408  825    0  111 1875    0     0    82  
104
C-428     63    0    0   80  100  695    0  162 2374    0   481   132  
369
C-434      0    0    0  269  261 1689    0 2923 3496    0     0     0  
  0
C-454     77    0    0  257  170  963    0  377 3984    0     0    90  
 96
C-465      0    0    0  234  406  860    0  428 1601    0     0     0  
  0
C-479    111    0    0  349  297 1538   51  494 3753    0    75   102  
 95

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