MCtest: Monte Carlo permutation test
In MAMA: Meta-Analysis of MicroArray

Description Usage Arguments Value Author(s) References See Also Examples

This function performs Monte Carlo permutation test to asses the statistical significance of R and Q statistics.

1	MCtest(RAN, RQ, nper = 100)

`RAN`	matrix of ranks to be permuted, columns refer to studies, rows refer to genes
`RQ`	observed values of R (average rank) and Q (heterogenity) - as produced by `compute.RQ`
`nper`	number of permutations

Returns a matrix with four columns. First (Second) column represents significance level of high (low) avarage rank. Third (fourth) represents significance level of high (low) heterogenity.

Ivana Ihnatova

Zintzaras, E., Ioannidis, J.P.A 2008 Meta-analysis for ranked discovery datasets: Theoretical framework and empirical demonstration for microarrays, Computational Biology and Chemistry 32, 39-47

rank.genes,compute.RQ

RANK<-cbind(sample(100), sample(100), sample(100))
RQ<-compute.RQ(RANK)
head(RQ)       
MCtest(RANK, RQ, nper=100)

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       r.star      q.star
[1,] 72.33333  928.666667
[2,] 48.33333 3980.666667
[3,] 52.00000 3614.000000
[4,] 21.33333  650.666667
[5,] 75.66667  752.666667
[6,] 33.66667    4.666667
100          R.high R.low Q.high Q.low
  [1,]   0.13  0.87   0.62  0.38
  [2,]   0.67  0.33   0.07  0.93
  [3,]   0.45  0.56   0.09  0.91
  [4,]   0.94  0.06   0.70  0.30
  [5,]   0.05  0.95   0.71  0.29
  [6,]   0.82  0.18   1.00  0.00
  [7,]   0.23  0.77   0.35  0.65
  [8,]   0.13  0.88   0.56  0.44
  [9,]   0.73  0.27   0.45  0.55
 [10,]   1.00  0.00   0.97  0.04
 [11,]   0.79  0.23   0.40  0.60
 [12,]   0.50  0.50   0.07  0.93
 [13,]   0.55  0.47   0.98  0.02
 [14,]   0.54  0.46   0.15  0.85
 [15,]   0.32  0.69   0.11  0.89
 [16,]   0.04  0.96   0.70  0.30
 [17,]   0.30  0.70   0.75  0.25
 [18,]   0.35  0.65   0.06  0.94
 [19,]   0.54  0.47   0.99  0.01
 [20,]   0.01  0.99   0.97  0.03
 [21,]   0.78  0.23   0.45  0.55
 [22,]   0.36  0.65   0.14  0.86
 [23,]   0.30  0.71   0.33  0.67
 [24,]   0.31  0.70   0.70  0.30
 [25,]   0.46  0.54   0.32  0.69
 [26,]   0.76  0.24   0.29  0.71
 [27,]   0.24  0.77   0.05  0.95
 [28,]   0.25  0.75   0.04  0.96
 [29,]   0.05  0.95   0.67  0.33
 [30,]   0.40  0.62   0.02  0.98
 [31,]   0.40  0.60   0.25  0.75
 [32,]   0.20  0.81   0.59  0.41
 [33,]   0.87  0.13   0.79  0.21
 [34,]   0.69  0.32   0.01  0.99
 [35,]   0.59  0.42   0.07  0.93
 [36,]   0.90  0.10   1.00  0.00
 [37,]   0.86  0.14   0.47  0.53
 [38,]   0.29  0.72   0.50  0.50
 [39,]   0.70  0.30   0.87  0.13
 [40,]   0.60  0.40   0.06  0.94
 [41,]   0.55  0.45   0.06  0.94
 [42,]   0.81  0.20   0.91  0.09
 [43,]   0.21  0.79   0.90  0.10
 [44,]   0.99  0.01   0.61  0.39
 [45,]   0.04  0.96   0.52  0.48
 [46,]   0.17  0.83   0.01  0.99
 [47,]   0.14  0.86   0.65  0.35
 [48,]   0.51  0.50   0.79  0.21
 [49,]   0.29  0.71   0.94  0.06
 [50,]   0.61  0.40   0.54  0.46
 [51,]   0.80  0.21   0.98  0.02
 [52,]   0.31  0.69   0.98  0.02
 [53,]   0.13  0.87   0.60  0.40
 [54,]   0.82  0.18   0.15  0.85
 [55,]   0.82  0.18   0.69  0.32
 [56,]   0.80  0.20   0.89  0.11
 [57,]   0.00  1.00   0.99  0.01
 [58,]   0.65  0.35   0.34  0.67
 [59,]   0.75  0.26   0.60  0.41
 [60,]   0.43  0.58   0.45  0.55
 [61,]   0.29  0.71   0.01  0.99
 [62,]   0.92  0.08   0.42  0.58
 [63,]   0.47  0.54   0.67  0.33
 [64,]   0.24  0.78   0.74  0.26
 [65,]   0.87  0.13   0.83  0.17
 [66,]   0.81  0.19   0.46  0.54
 [67,]   0.27  0.74   1.00  0.00
 [68,]   0.85  0.16   0.86  0.14
 [69,]   0.11  0.89   0.18  0.83
 [70,]   0.98  0.02   0.99  0.02
 [71,]   0.80  0.23   0.37  0.63
 [72,]   0.83  0.17   0.49  0.51
 [73,]   0.02  0.98   0.71  0.29
 [74,]   0.61  0.40   0.56  0.44
 [75,]   0.69  0.32   0.99  0.02
 [76,]   0.63  0.37   0.00  1.00
 [77,]   0.18  0.82   0.22  0.78
 [78,]   0.13  0.88   0.47  0.55
 [79,]   0.57  0.44   0.32  0.68
 [80,]   0.23  0.77   0.71  0.29
 [81,]   0.92  0.09   0.80  0.20
 [82,]   0.03  0.97   0.81  0.19
 [83,]   0.93  0.08   0.39  0.61
 [84,]   0.77  0.23   0.16  0.84
 [85,]   0.97  0.03   0.71  0.29
 [86,]   0.91  0.09   0.56  0.44
 [87,]   0.15  0.85   0.37  0.63
 [88,]   0.71  0.29   0.18  0.82
 [89,]   0.77  0.23   0.18  0.82
 [90,]   0.58  0.42   0.38  0.62
 [91,]   0.61  0.39   0.10  0.90
 [92,]   0.09  0.91   0.42  0.58
 [93,]   0.65  0.35   0.15  0.85
 [94,]   0.40  0.60   0.67  0.33
 [95,]   0.88  0.13   0.37  0.63
 [96,]   0.06  0.95   0.73  0.27
 [97,]   0.18  0.84   0.82  0.18
 [98,]   0.31  0.70   0.18  0.82
 [99,]   0.50  0.51   0.53  0.47
[100,]   0.16  0.85   0.75  0.25
Warning message:
system call failed: Cannot allocate memory