Table 2

Average AUC for RMA, RMA-noBG, MAS 5.0, dChip, and PLIER for detection of spiked-in genes in the Affymetrix Latin Square spikein experiments, according to the value of d, which is related to the log base 2 fold change between experiments.

d

DFCM

RMA

RMA-noBG

MAS 5

dChip

PLIER


Average AUC for the HG-U95Av2 Latin Square Spike-In Data Set


1

0.732

0.715

0.721

0.063

0.572

0.062

2

0.871

0.869

0.918

0.167

0.803

0.316

3

0.936

0.935

0.935

0.484

0.886

0.629

4

0.997

0.994

0.986

0.798

0.948

0.769

5

1.000

0.999

0.999

0.916

0.980

0.853

6

1.000

1.000

1.000

0.967

0.987

0.876

7

1.000

1.000

1.000

0.981

0.999

0.876

Average AUC for the HG-U133A Latin Square Spike-In Data Set

1

0.768

0.738

0.734

0.060

0.600

0.365

2

0.858

0.831

0.812

0.307

0.709

0.752

3

0.935

0.904

0.908

0.561

0.811

0.883

4

0.934

0.964

0.964

0.837

0.913

0.951

5

0.983

0.990

0.983

0.939

0.971

0.985

6

0.999

0.998

0.996

0.968

0.989

0.994

7

0.999

0.999

0.999

0.978

0.972

0.996


Larger values of d correspond to larger fold changes among spiked-in transcripts between pairs of experiments. Eighteen spike-in probes sets were used for the HG-U95Av2 experiment, and 64 spiked-in probe sets were used for the HG-U133A to calculate true and false positives, as discussed in Methods. To calculate the AUCs, the number of false positives was set to 100 for the HG-U95Av2 experiment, and 200 for the HG-U133a experiment. Numbers in bold indicate the best value for each row.

Chen et al. BMC Genomics 2009 10(Suppl 1):S19   doi:10.1186/1471-2164-10-S1-S19

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