Table 2.
Preprocessing overview
| method | package | function | log2 | σ | reference |
|---|---|---|---|---|---|
| RMA | affy | Expresso | yes | yes | [55] |
| mgMOS | puma | justmgMOS | yes | yes | [56] |
| mmgMOS | puma | justmmgMOS | yes | yes | [57] |
| dChip | affy | expresso | no | yes | [58] |
| MAS5.0 | affy | expresso | no | no | [59] |
| Rosetta | - | - | - | - | [11] |
The column package indicates which R package was used to obtain the expression values, while the column function provides the name of the function used from the package. Column log2 indicates if the expression estimates as returned by the function are already on log2 scale or not. The column σ indicates if the function directly computes uncertainty information or not.