# Excel Worksheets for Array Data - Excel

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```					Table 2. This table supplies the threshold values for t for the joint probability approach. These values are provided for those us
The value of t presented on the table is that minimum per comparison value of t allowed for a particular expression difference to
N = the number of elements in the array, FDR = 0.95 (i.e. phi =0.05), and k = the maximum number of false positives allowed.
Although increasing k increases the number of expected false positives, it will also increase the number of candidate genes for
The value of t also depends on the degrees of freedom in the analysis. Two sets of t are provided: when 4 biological replicates
and when 6 biological replicates are carried out for a total 20 degrees of freedom. We are in the process of generating similar
5 biological replicates (16 degrees of freedom).
k (12 degr
Arrays                                         N             0       1       2       3      4      5      6       7
E. Coli Target                                  7312 7.02 5.725            5.2 4.895 4.675 4.515 4.38 4.275
GPL176 Arabidopsis                              8256 7.13 5.795 5.27 4.965 4.75 4.585 4.45 4.34
Human Genome Focus Array                        8793 7.265 5.84 5.315                5 4.785 4.62 4.485 4.38
Yeast Genome S98 Array                          9335 7.265 5.87 5.35 5.035 4.82 4.655 4.52 4.41
Drosophila Genome Array                        14010 7.645 6.145 5.605 5.285 5.06 4.895 4.76 4.645
C. elegans Genome Array                        22625 7.955 6.49 5.905 5.58 5.35 5.18 5.04 4.93
Arabidopsis ATH1 Genome Array                  22810 7.955 6.49 5.925 5.595 5.36 5.185 5.045 4.93
Barley Genome Array                            22840 7.955 6.49 5.925 5.595 5.36 5.185 5.05 4.93
Rat Expression Set 230                         31256 8.505         6.7 6.12 5.795 5.55 5.38 5.235 5.12
Human Genome U133 Plus 2.0 Array               44928 8.505 7.02 6.365 6.025 5.795 5.605 5.46 5.345
Mouse Expression Set 430                       45265 8.505 7.02 6.365 6.025 5.795 5.615 5.47 5.35

k (20 degr
Arrays                                        N            0       1        2       3        4        5        6        7
E. Coli Target                                 7312   5.705    4.855   4.495    4.275   4.115    3.995       3.9   3.815
GPL176 Arabidopsis                             8256   5.775    4.905   4.545    4.325    4.17     4.05     3.95     3.87
Human Genome Focus Array                       8793   5.855    4.935   4.575    4.355   4.195    4.075    3.975    3.895
Yeast Genome S98 Array                         9335   5.855     4.96      4.6    4.38    4.22       4.1   4.005     3.92
Drosophila Genome Array                       14010    6.09     5.14   4.775    4.555   4.395    4.275    4.175    4.095
C. elegans Genome Array                       22625   6.275    5.365    4.98     4.76      4.6    4.48     4.38       4.3
Arabidopsis ATH1 Genome Array                 22810   6.275    5.365   4.995     4.77   4.605    4.485    4.385    4.305
Barley Genome Array                           22840   6.275    5.365   4.995     4.77   4.605    4.485     4.39    4.305
Rat Expression Set 230                        31256      6.6   5.505   5.125    4.905    4.74     4.62     4.52     4.44
Human Genome U133 Plus 2.0 Array              44928      6.6   5.705   5.285     5.06   4.905    4.775    4.675    4.595
Mouse Expression Set 430                      45265      6.6   5.705   5.285     5.06   4.905    4.785     4.68       4.6
es are provided for those users who use the provided Excel worksheets to analyze their array data.
ular expression difference to be called significant given the following variables:
of false positives allowed.
ber of candidate genes for follow-up expression analysis.
when 4 biological replicates are carried out for a total of 12 degrees of freedom
cess of generating similar tables for 3 biological replicates (8 degrees of freedom) as well as

k (12 degrees of freedom)
8      9    10      11   12       13      14     15      16     17      18      19       20
4.18     4.1 4.03 3.96 3.905        3.85   3.805   3.76   3.715   3.68    3.64   3.605   3.575
4.25 4.165 4.1 4.03 3.97            3.92    3.87   3.83    3.78   3.75   3.705    3.67    3.64
4.285     4.2 4.13 4.065 4.005      3.955   3.905   3.86   3.815   3.78    3.74   3.705   3.675
4.315 4.235 4.17        4.1 4.04    3.985    3.94   3.89    3.85   3.81   3.775    3.74   3.705
4.55 4.465 4.4 4.325 4.27          4.215   4.165   4.12   4.075   4.04       4   3.965    3.93
4.83 4.745 4.67        4.6 4.54    4.485   4.435   4.39   4.345   4.31   4.265    4.23   4.195
4.835 4.75 4.68 4.605 4.545          4.49    4.44    4.4    4.35   4.31    4.27   4.235      4.2
4.835 4.75 4.68 4.605 4.545          4.49    4.44    4.4    4.35   4.31   4.275   4.235      4.2
5.02 4.935 4.86 4.79 4.73          4.675   4.625   4.58    4.53   4.49    4.45   4.415    4.38
5.255 5.155 5.08 5.01 4.945         4.885    4.84   4.79    4.74    4.7    4.66   4.625    4.59
5.25 5.16 5.08 5.015 4.95          4.895    4.84   4.79   4.745   4.71   4.665    4.63   4.595

k (20 degrees of freedom)
8      9    10      11    12      13      14     15      16     17      18      19      20
3.745 3.685 3.63 3.58 3.535          3.49   3.455   3.42   3.385   3.36   3.325   3.295    3.27
3.795 3.735 3.68 3.63 3.585         3.545   3.505   3.47   3.435   3.41   3.375    3.35   3.325
3.825 3.76 3.71 3.655 3.61           3.57   3.535    3.5   3.465   3.44   3.405   3.375    3.35
3.85 3.79 3.74 3.685 3.64          3.595    3.56   3.53    3.49   3.46    3.43   3.405   3.375
4.025 3.96 3.91 3.855 3.815          3.77   3.735    3.7   3.665   3.64   3.605    3.58   3.555
4.23 4.17 4.11 4.06 4.02           3.975    3.94   3.91    3.87   3.84    3.81   3.785    3.76
4.235 4.17 4.12 4.065 4.02           3.98    3.94   3.91   3.875   3.85   3.815    3.79   3.765
4.235 4.17 4.12 4.065 4.02           3.98   3.945   3.91   3.875   3.85   3.815    3.79   3.765
4.365 4.305 4.25        4.2 4.155   4.115    4.08   4.04    4.01   3.98    3.95   3.925   3.895
4.535 4.465 4.41 4.36 4.31           4.27   4.235    4.2   4.165   4.14   4.105    4.08    4.05
4.53 4.465 4.41 4.36 4.315         4.275   4.235    4.2    4.17   4.14    4.11    4.08   4.055

```
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