[BioC] Why is my matrix transposed?

[Balasubramanian Ganesan]

Dear all
I am running R-2.6.2 on a PowerPC PowerBook-G4.
I am using the following method to normalize my data.

 >library(affy)
 >eset=justRMA()

I used two different ways of writing out the eset data.
 >write.table(eset,file="abc.txt",sep="\t") # produces a table with  
probe IDs as cols and sample names as rows (order of data is transposed)

But if I use
 >write.exprs(eset,file="abc2.txt") # produces a table with probe IDs  
as rows and sample names as col headers, which is what we want.

Why do I see this discrepancy? I have always used "Write.table" in  
the past and has always worked for me upto R-2.5. I started having  
this issue only with R-2.6 and have it with both versions of 2.6.

Balasubramanian Ganesan
Research Assistant Professor
Center for Integrated BioSystems
Utah State University
4700 Old Main Hill
Logan UT 84322
balag at cc.usu.edu