Table 3.
Normalization | Background Correction Methods | |||
DFCM | RMA | None | MAS 5 | |
Loess | 86 | 87 | 88 | 57 |
Quantile | 48 | 47 | 50 | 60 |
Scale | 83 | 80 | 76 | 24 |
To examine the effect of normalization on the results, quantile normalization, scale normalization (as defined for the MAS 5.0 algorithm) or loess was used in combination with each of the background methods discussed in this paper. All methods (except for MAS 5.0) used median polish summarization. Differentially expressed genes were selected using two-sample t-tests. The methods GCRMA, dChip and PLIER could not be used because their background correction, normalization, and summarization algorithms cannot be separated easily.