Table 8.

Summary of microarray data generation methods. The following table was compiled with reference to the sources of each microarray data set

DataSet Name	Description of Data Generation Method
Haslett et al. (2002)	24 quadriceps biopsies (12 from DMD patients, 12 from controls). RNA extraction with Trizol, Hybridized to HG-U95Av2 GeneChips. GeneChip scanning with Affymetrix/Hewlett–Packard G2500A Gene Array Scanner. Expression values calculated with Affymetrix GeneChip Ver. 5.0 software
Pescatori et al. (2007)	36 quadriceps biopsies (24 from DMD patients, 12 from controls). RNA extraction with Trizol, Hybridized to HG-U133A GeneChips, GeneChip scanning with Affymetrix G2500 GeneChip scanner. Raw data processed with the log scale robust multiarray analysis (rma) procedure by Irizarry et al. (2003), then normalized and background-corrected. Genes with little variation (having less than 20% of arrays having variation greater than 1.5 times the median) across arrays were excluded from the data set
Golub et al. (1999)	38 leukemia samples from bone marrow aspirates (27 childhood ALL, 11 adult AML) and 34 independent leukemia samples (24 bone marrow, 10 peripheral blood; 20 childhood ALL, 4 adult AML, 10 childhood AML). Extracted with Trizol (Gibco/BRL), RNAqueous reagents (Ambion) or aqueous extraction (Qiagen). Hybridized to HU-6800 GeneChips. No mention of data processing methods
Armstrong et al. (2002)	48 leukemia samples from peripheral blood or bone marrow (24 ALL, 24 AML). Extracted with Trizol. Hybridized to HG-U95Av2 GeneChips. Expression values calculated with Affymetrix GeneChip software. Raw data normalized with a linear scaling method
Yeoh et al. (2002)	42 bone marrow samples (15 BCR-ABL, 27 E2A-PBX1). Extracted with Trizol. Hybridized to HG-U95Av2 GeneChips. GeneChip scanning with a laser confocal scanner (Agilent). Expression values calculated with Affymetrix Microarray software v.4.0. Average intensity difference (AID) values of each sample were normalized
Ross et al. (2004)	33 bone marrow (BM) aspirates or peripheral blood (PB) samples (15 BCR-ABL, 18 E2A-PBX1). Hybridized to HG-U133A GeneChips. Expression values calculated with Affymetrix Microarray Suite 5.0 (MAS 5.0). Raw data scaled to 500 with global methods. Parameters for the determination of detection values (present, marginal, or absent) were set to default values