Table 1

Summary of sequence correction models
Model
 Formalism
 Number of parameters
 Average R2
 Average adjusted R2
 Number of transcriptionally active regions
Uncorrected
 NA
 NA
 NA
 NA
 47,463
GC
 log I = β0 + βGC(NC + NG)
 2
 0.0293
 0.0284
 52,384
Nucleotide-specific
 log I = β0 + βANA + βCNC + βGNG
 4
 0.0412
 0.0373
 53,982
Bilinear
 log I = β0 +

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 41 = 36 + 4 + 1
 0.0980
 0.0604
 61,731
Full Position-specific
 log I = β0 +

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 109 = 36 × 3 + 1
 0.1709
 0.0703
 71,400

Overview of the models used to relate probe sequence to signal intensity. The Full Position-specific model has the highest R2 and also the highest adjusted R2, indicating that overfitting is not a concern. The rightmost column shows the number of probed loci classified as transcriptionally active, which varies greatly with the sequence model used. NA, not applicable.

Halasz et al. Genome Biology 2006 7:R59   doi:10.1186/gb-2006-7-7-r59

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