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Old 01-23-2017, 10:12 AM   #1
lupid
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Location: chile

Join Date: Mar 2015
Posts: 54
Default 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
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Old 01-23-2017, 10:27 AM   #2
lupid
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Location: chile

Join Date: Mar 2015
Posts: 54
Default file

Here is a short version of the outcome
Attached Files
File Type: txt result.txt (2.0 KB, 2 views)
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Old 01-23-2017, 11:01 AM   #3
wdecoster
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Location: Antwerp, Belgium

Join Date: Oct 2015
Posts: 96
Default

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.
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