Evaluating methods for ranking differentially expressed genes applied to microArray quality control data

BMC Bioinformatics

Table 3 List of best methods with different threshold settings for defining DEGs

Technology	TAQ	TAQ	TAQ	TAQ	TAQ	TAQ	TAQ	TAQ	GEX	GEX	GEX
#DEGs	100	200	300	400	500	600	700	800	50	100	150
AFX
AB_FDR	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD
AB_AD	RP	AD	AD	RP	RP	samT	ibmT	WAD	RP	WAD	WAD
CD_FDR	AD	RP	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD
CD_AD	AD	RP	RP	RP	RP	RP	ibmT	WAD	ibmT	WAD	WAD
ABI
AB_FDR	WAD	ibmT	WAD	WAD	WAD	WAD	WAD	ibmT	ibmT	ibmT	ibmT
AB_AD	RP	RP	RP	RP	RP	samT	WAD	ibmT	samT	ibmT	ibmT
CD_FDR	WAD	WAD	WAD	WAD	ibmT	ibmT	ibmT	ibmT	WAD	ibmT	ibmT
CD_AD	RP	RP	RP	samT	shrT	WAD	ibmT	ibmT	ibmT	ibmT	ibmT
AG1
AB_FDR	RP	WAD	WAD	ibmT	WAD	WAD	WAD	WAD	WAD	WAD	WAD
AB_AD	RP	RP	RP	RP	RP	RP	ibmT	WAD	FC	ibmT	WAD
CD_FDR	shrT	WAD	WAD	WAD	WAD	WAD	WAD	WAD	ibmT	WAD	WAD
CD_AD	FC	RP	RP	RP	RP	RP	WAD	WAD	ibmT	ibmT	WAD
GEH
AB_FDR	RP	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD
AB_AD	RP	RP	RP	RP	RP	shrT	WAD	WAD	WAD	WAD	WAD
CD_FDR	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD
CD_AD	samT	RP	RP	RP	RP	WAD	WAD	WAD	WAD	WAD	WAD
ILM
AB_FDR	AD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD
AB_AD	RP	RP	RP	RP	RP	RP	RP	WAD	RP	WAD	WAD
CD_FDR	RP	RP	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD	WAD
CD_AD	AD	RP	RP	RP	RP	RP	WAD	WAD	RP	WAD	WAD

ISSN: 1471-2105