extracting VennDiagram data for sequence information

Question

[tchakraborty83]

Can anyone guide me to extract venndiagram data? I am quite new to R and I am trying to extract the vennDiagram data to get the sequence ID or information. However, i am stuck. Some help will be appreciated. Following are my commands:

>data1 <- read.delim(RMAfiles[1], header=TRUE)
> #1 and 2, 1 and 3, 1 and 4, 1 and 5 and 1 and 6
> expressionMatrix <- matrix(data=NA, nrow=nrow(data1), ncol=6, dimnames=list(data1[,"PROBE_ID"], RMAfiles))
> for (i in 1:6){
+     dataI <- read.delim(RMAfiles[i], header=TRUE)
+     expressionMatrix[,i] <- log2(dataI[,"PM"])    
+ }
>head(expressionMatrix)
> write(expressionMatrix)
> ratio1 <- expressionMatrix[,5] - expressionMatrix[,6]
> ratio2 <- expressionMatrix[,5] - expressionMatrix[,1]
> ratio3 <- expressionMatrix[,5] - expressionMatrix[,2]
> ratio4 <- expressionMatrix[,5] - expressionMatrix[,3]
> ratio5 <- expressionMatrix[,5] - expressionMatrix[,4]
> XYD3 <- (ratio1 <= -11)
> ERab2D3 <- (ratio2 <= -11)
> ERaD3 <- (ratio3 <= -11)
> ERb2D3 <- (ratio4 <= -11)
> ERb2KDD3 <- (ratio5 <= -11)
> C52 <-cbind(XYD3, ERab2D3, ERaD3, ERb2D3, ERb2KDD3)
> c <-vennCounts(C52)
> vennDiagram(c)

Regards Tapas

[GouthamAtla]

can you format the code part properly with line breaks ?

[ivivek_ngs]

I believe this is expression matrix with row.names as genes right? . You should have one one matrix where you are trying to calculate the fold change between your columns for particular genes right? If so Then use row.names=1 while reading the files so that the genes are in the row. Take a look at this link to see if your expression matrix is properly created. Also try to put the output of head(expressionMatrix) so that we can see what is it.