| Input: labeled gene expression matrix |
| Desired size of differential gene list |
| Steps: |
| Calculate two-sample (unpaired) -statistics as in equation . |
| Re-index genes such that . |
| Create vector with elements ( scores) in order of ascending magnitude. |
| Set (default value ). Set first elements of to zero ( partition)†. |
| Convert to by subtracting each gene's average response within each treatment group. |
| Compute sample correlation matrix of (Section 4.4). |
| Find as in (21). (See discussion of product in Section 5.2.)
|
| Create a list of re-ranked genes in the descending order of the values , in which is the th |
| element of . ‡ |
| Report genes with the largest re-ordered scores as statistical discoveries. |
| Output: List of (experimentally-determined) most differentially-expressed genes following |
| the decorrelation processing. |
| †For convenience, it is assumed that is chosen so that is an integer. |
| ‡The original vector, , of raw -scores (Step ) is ordered by ascending values of . This ordering |
| simplifies the definitions of certain quantities in the formal developments. Note: however, that the |
| output list (Steps and ) is created according to descending values. This is a more natural |
| ordering for the end result as we are interested in only the largest values. |
