Table 2. Improved detection of differentially expressed genes with multiple scans (TSA technology).
| 2 scans | 4 scans | 6 scans | 8 scans | 10 scans | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Mean | Max | Mean | Max | Mean | Max | Mean | Max | Mean | Max | |
| Over-expressed | ||||||||||
| FP | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 1 (1) | 1 (1) | 0 (0) | 1 (1) | 0 (0) | 0 (0) |
| CFP | – | – | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| NFP | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 |
| FN | 110 (74) | 90 (61) | 154 (104) | 131 (89) | 184 (124) | 137 (93) | 198 (134) | 158 (107) | 207 (140) | 169 (114) |
| CFN | – | – | 107 | 85 | 152 | 117 | 175 | 131 | 189 | 150 |
| NFN | 110 | 90 | 47 | 46 | 31 | 17 | 21 | 16 | 14 | 14 |
| Under-expressed | ||||||||||
| FP | 2 (2) | 2 (2) | 2 (2) | 2 (2) | 1 (1) | 2 (2) | 2 (2) | 2 (2) | 2 (2) | 2 (2) |
| CFP | – | – | 2 | 2 | 0 | 2 | 1 | 2 | 1 | 2 |
| NFP | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| FN | 175 (164) | 157 (147) | 214 (200) | 198 (185) | 229 (214) | 191 (179) | 263 (246) | 212 (198) | 255 (238) | 244 (228) |
| CFN | – | – | 170 | 149 | 203 | 173 | 223 | 179 | 241 | 197 |
| NFN | 175 | 157 | 44 | 49 | 22 | 17 | 32 | 23 | 6 | 21 |
A cDNA microarray was subjected to a competitive hybridisation with normal and dystrophic muscle RNAs. Hybridisation signals have been generated with TSA technology and the microarray was subjected to single and then to increasing numbers of laser scans, as indicated. After a single scan of the microarray, 149 over- and 107 under-expressed transcripts in normal versus dystrophic muscle RNA were found. The additional differentially expressed transcripts obtained after microarray analysis with ΣPOT software are reported and classified as in the footnotes of Table 1.