[BioC] Why is my matrix transposed?

Balasubramanian Ganesan balag at cc.usu.edu
Fri Mar 7 18:00:21 CET 2008

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


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

More information about the Bioconductor mailing list