Table 1. Standard microarray data formats handled by limma.
| Software | Vendor | Channels |
|---|---|---|
| Agilent Feature Extraction | Agilent Technologies | 1/2 |
| ArrayVision | GE Healthcare | 1/2 |
| BlueFuse | BlueGnome | 1/2 |
| GenePix | Molecular Devices | 1/2 |
| BeadScan/GenomeStudio | Illumina Inc. | 1 |
| ImaGene | BioDiscovery | 1/2 |
| QuantArray | PerkinElmer Life Sciences | 1/2 |
| ScanArray Express | PerkinElmer Life Sciences | 1/2 |
| SMD | Stanford | 1/2 |
| Spot | CSIRO | 1/2 |
Data output by the above software can be read-in using read.maimages or read.ilmn. limma can read files in other formats, provided the user provides the names of the columns containing foreground and background intensities.