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:
And then in the .txt I get one column with a "DEX" parametre, but I can't find what it mean. 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)
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