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

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

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