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  • EdgeR and DEX

    Hi to all I´m currently working with a pre-made R script to RNA-Seq using EdgeR, but I dont quite understand one of the outcome columns, please help.

    This is the script:

    Code:
    ################M3E_M5FE#######
    head(M3E_M5FE)
    
    rownames(M3E_M5FE)=M3E_M5FE$`V1`
    M3E_M5FE$`V1`=NULL
    M3E_M5FE$`V1`=NULL
    M3E_M5FE$`V1`=NULL
    M3E_M5FE$`V1`=NULL
    M3E_M5FE$`V1`=NULL
    M3E_M5FE$`V1`=NULL
    M3E_M5FE$`V1`=NULL
    
    colnames(M3E_M5FE$`V1`=NULL)=c("M3BE3","M3FE2","M3FE3","M5FE2","M5FE3","M5FE4")
    
    
    #Generar diseno (15 replicas para estado 1 y 15 para estado 2)
    group_EdgeR=c((rep(1,3)),(rep(2,3)))
    group_EdgeR
    
    
    
    
    #####Generar lista tipo DGE#
    y_EdgeR=DGEList(counts=M3E_M5FE, group=group_EdgeR)
    
    #Confirmar diseño
    #y_EdgeR$samples
    
    #Filtro por CPM (usa CPM para considerar diferencias entre librerias)
    keep_EdgeR <- rowSums(cpm(y_EdgeR)>1) >= 2
    y_EdgeR <- y_EdgeR[keep_EdgeR, , keep.lib.sizes=FALSE]
    
    #Estimacion de dispersion de datos
    y_EdgeR=estimateCommonDisp(y_EdgeR)
    
    #Calculo de FDR ajustado (o P-Adjusted)
    y_EdgeR=estimateTagwiseDisp(y_EdgeR)
    
    #Extracción de genes expresados diferencialmente
    et_EdgeR=exactTest(y_EdgeR)
    resEdgeR_EdgeR=topTags(et_EdgeR,n=Inf)
    ResultsTEMP_EdgeR=as.data.frame(resEdgeR_EdgeR)
    ResultsTEMP_EdgeR$DEX=ifelse(ResultsTEMP_EdgeR$FDR <= 0.05, 1,0)
    
    #Tabla resultado final
    ResultsTEMP_EdgeR
    
    getwd()
    write.table(ResultsTEMP_EdgeR, "ResultadosEdger_M3E_M5FE_R.txt", sep="\t", quote=F, row.names=T, col.names=T)
    And then in the .txt I get one column with a "DEX" parametre, but I can't find what it mean. please help

  • #2
    file

    Here is a short version of the outcome
    Attached Files

    Comment


    • #3
      That field is created here:

      Code:
      ResultsTEMP_EdgeR$DEX=ifelse(ResultsTEMP_EdgeR$FDR <= 0.05, 1,0)
      So: If the FDR is below 0.05 put a 1 in DEX, if not put a 0.

      Comment

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