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Table 2 Power by Intensity Range.

From: Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays

  

Power by Intensity Quartile

 

Data

Method

Q1

Q2

Q3

Q4

Overall Power

Golden Spike

ANOVA

0.096

0.192

0.295

0.465

0.262

 

Combined P

0.144

0.315

0.413

0.568

0.360

 

Cyber-T

0.042

0.141

0.259

0.477

0.230

 

Median t

0.141

0.306

0.404

0.556

0.352

 

Moderated t

0.060

0.159

0.265

0.396

0.220

 

Original t

0.006

0.009

0.021

0.033

0.017

Gene Logic Tonsil

ANOVA

0.341

0.619

0.829

0.577

0.591

 

Combined P

0.390

0.646

0.867

0.615

0.629

 

Cyber-T

0.374

0.624

0.790

0.566

0.588

 

Median t

0.368

0.630

0.851

0.599

0.612

 

Moderated t

0.258

0.597

0.746

0.549

0.537

 

Original t

0.203

0.547

0.713

0.473

0.483

Affymetrix Latin Square

ANOVA

0.418

0.819

0.915

0.813

0.741

 

Combined P

0.518

0.887

0.945

0.895

0.811

 

Cyber-T

0.646

0.925

0.986

0.972

0.882

 

Median t

0.591

0.916

0.982

0.967

0.864

 

Moderated t

0.584

0.888

0.968

0.927

0.841

 

Original t

0.518

0.847

0.941

0.872

0.795

  1. This table shows the power for each of the four intensity quartiles as well as the overall power for each of the datasets and methods. The power is calculated as the proportion of true positives that were detected while maintaining an overall false discovery rate of 0.05 or less.
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BMC Genomics

ISSN: 1471-2164

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