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Table 4 The mean square errors of estimated gene expression levels for simulated cDNA microarray data with differentially expressed genes inserted under the high expression levels conditions.

From: Evaluating different methods of microarray data normalization

Percentage of DEG

 

Sinusoid

Banana

Mixed

 

Method

25% Quantile

Median

75% Quantile

25% Quantile

Median

75% Quantile

25% Quantile

Median

75% Quantile

5%

Loess

0.00038

0.00039

0.00040

0.00081

0.00087

0.00094

0.04633

0.04639

0.04648

 

Splines

0.00035

0.00036

0.00037

0.00079

0.00086

0.00092

0.04658

0.04665

0.04674

 

Wavelets

0.00033

0.00034

0.00035

0.00115

0.00121

0.00129

0.04643

0.04650

0.04660

 

Kernel

0.03781

0.03782

0.03783

0.16417

0.16453

0.16513

0.17428

0.17436

0.17447

 

SVR

0.00031

0.00032

0.00033

0.00080

0.00087

0.00092

0.04527

0.04534

0.04544

10%

Loess

0.00146

0.00153

0.00168

0.00145

0.00156

0.00167

0.04733

0.04748

0.04758

 

Splines

0.00142

0.00149

0.00160

0.00147

0.00157

0.00168

0.04756

0.04767

0.04779

 

Wavelets

0.00140

0.00147

0.00159

0.00160

0.00170

0.00182

0.04725

0.04736

0.04748

 

Kernel

0.02662

0.03454

0.03789

0.23086

0.23135

0.23245

0.18441

0.19003

0.19176

 

SVR

0.00126

0.00133

0.00144

0.00142

0.00154

0.00166

0.04678

0.04687

0.04696

15%

Loess

0.00203

0.00217

0.00234

0.00199

0.00212

0.00224

0.04963

0.04976

0.04991

 

Splines

0.00198

0.00211

0.00223

0.00200

0.00211

0.00222

0.04987

0.05001

0.05014

 

Wavelets

0.00196

0.00209

0.00224

0.00219

0.00240

0.00257

0.04975

0.04989

0.05001

 

Kernel

0.02318

0.02992

0.03729

0.17578

0.20066

0.22763

0.18472

0.18898

0.18923

 

SVR

0.00178

0.00190

0.00200

0.00170

0.00180

0.00189

0.04885

0.04898

0.04912

20%

Loess

0.00260

0.00275

0.00293

0.00259

0.00272

0.00289

0.04917

0.04930

0.04944

 

Splines

0.00254

0.00268

0.00286

0.00260

0.00270

0.00289

0.04933

0.04946

0.04961

 

Wavelets

0.00253

0.00267

0.00284

0.00289

0.00304

0.00320

0.04919

0.04933

0.04947

 

Kernel

0.02224

0.02819

0.03468

0.16500

0.17817

0.20385

0.18207

0.18716

0.19141

 

SVR

0.00226

0.00239

0.00255

0.00247

0.00258

0.00272

0.04839

0.04850

0.04863

40%

Loess

0.00501

0.00520

0.00545

0.00518

0.00538

0.00555

0.04980

0.04999

0.05020

 

Splines

0.00498

0.00519

0.00539

0.00520

0.00538

0.00558

0.05002

0.05022

0.05038

 

Wavelets

0.00496

0.00517

0.00537

0.00535

0.00551

0.00572

0.04984

0.05004

0.05020

 

Kernel

0.02155

0.02487

0.02810

0.18250

0.20140

0.22296

0.17524

0.18072

0.18433

 

SVR

0.00446

0.00467

0.00489

0.00464

0.00483

0.00505

0.04809

0.04829

0.04860

  1. DEG: Differentially expressed genes