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Table 1 The number of differentially expressed genes. Number of genes significant (Ttest p < 0.05) up or down regulated between air control and ethylene or low-light treatment in six different algorithms. The number of biological replicates for each treatment is three. The number of probe pairs per chip is 22746.

From: How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results

Method

Control – ethylene

Control – Low-light

MAS 5.0

2201

2384

dChip PMMM

2559

2665

dChip PM

2435

2583

RMA

2470

2705

GC-RMA

2258

2411

PDNN

2972

3262