Table 1. Improved detection of differentially expressed genes with multiple scans (RT labelling).
| 2 scans | 4 scans | 6 scans | 8 scans | 10 scans | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Mean | Max | Mean | Max | Mean | Max | Mean | Max | Mean | Max | |
| Over-expressed | ||||||||||
| FP | 26 (13) | 19 (10) | 21 (11) | 21 (11) | 24 (12) | 19 (10) | 20 (10) | 30 (15) | 24 (12) | 24 (12) |
| CFP | – | – | 19 | 15 | 18 | 13 | 15 | 13 | 16 | 14 |
| NFP | 26 | 19 | 2 | 6 | 3 | 2 | 1 | 7 | 2 | 2 |
| FN | 18 (9) | 41 (21) | 37 (19) | 36 (18) | 36 (18) | 53 (27) | 50 (25) | 18 (9) | 34 (17) | 29 (15) |
| CFN | – | – | 15 | 20 | 22 | 20 | 24 | 17 | 34 | 15 |
| NFN | 18 | 41 | 10 | 5 | 4 | 10 | 4 | 0 | 0 | 3 |
| Under-expressed | ||||||||||
| FP | 6 (19) | 7 (22) | 2 (6) | 5 (16) | 2 (6) | 3 (9) | 4 (13) | 3 (9) | 4 (13) | 1 (3) |
| CFP | – | – | 2 | 4 | 2 | 3 | 2 | 2 | 2 | 1 |
| NFP | 6 | 7 | 0 | 1 | 1 | 0 | 1 | 0 | 1 | 1 |
| FN | 7 (22) | 12 (38) | 13 (41) | 15 (47) | 14 (44) | 18 (56) | 23 (72) | 15 (47) | 20 (63) | 20 (63) |
| CFN | – | – | 4 | 7 | 10 | 9 | 13 | 11 | 17 | 14 |
| NFN | 7 | 12 | 9 | 8 | 3 | 8 | 7 | 3 | 2 | 3 |
A cDNA microarray was subjected to competitive hybridisation with skeletal muscle and heart RNAs, both made fluorescent by RT labelling and subjected to single and then to increasing numbers of laser scans, as indicated. After analysis with ΣPOT and the programs described in Materials and Methods, the differentially expressed transcripts were counted. The single scan analysis showed 200 over- and 31 under-expressed transcripts in skeletal muscle versus heart. The absolute and percentage (in parentheses) increments of over- and under-expressed transcripts with respect to the first scan are indicated for every two scans added. The results of ΣPOT analysis according to the mean pixel (Mean) or the maximum pixel (Max) calculation principle are reported separately in two flanking columns.
FP = false positive; FN = false negative; CFP and CFN = consistent false positive and negative; NFP and NFN = novel false positive and negative. See text for the description and discussion of this classification.