Table 4

Comparison of variance of log ratios for control spots in SW480/620 experiments

Control spot

Number of replicate spots per slide

Global lowess

P-lowess

S-lowess

OLIN

OSLIN

SS-DNA

48

6.46

3.33

4.03

1.90

2.82

Cot-1 DNA

12

4.34

4.10

5.07

2.90

3.73

Rice DNA

12

12.0

4.34

5.03

2.35

2.79

The average within-slide variance (× 10^-2) of log ratios M of control spots is shown after applying different normalization schemes. The three types of control spots derived from genomic DNA were used: salmon sperm (SS) DNA; Cot-1 DNA; rice DNA. Their intensities were above background as a result of nonspecific cross-hybridization. The locations of the replicated control spots were spatially distributed across the array. Comparison of corresponding log ratios M thus provides a measure for the spatial consistency of results produced by normalization.

Futschik and Crompton Genome Biology 2004 5:R60   doi:10.1186/gb-2004-5-8-r60