[BioC] Why is my matrix transposed?
Kasper Daniel Hansen
khansen at stat.Berkeley.EDU
Sat Mar 8 03:09:51 CET 2008
This probably happened because the object returned from justRMA
changed from a exprSet to an ExpressionSet and that these two classes
have different coercion rules But for both class exprs(OBJECT) returns
the same matrix - hence write.exprs is stable.
So to summarize, my guess is that it has to do with changes in the
On Mar 7, 2008, at 12:00 PM, James W. MacDonald wrote:
> Balasubramanian Ganesan wrote:
>> 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
>> 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.
> You get this discrepancy because write.table() isn't designed to use
> S4 object. From ?write.table
> x: the object to be written, preferably a matrix or data frame.
> If not, it is attempted to coerce 'x' to a data frame.
> So by using write.table() rather than the function specifically
> to do what you want, you are assuming that the coercion of an
> ExpressionSet to data.frame will end up doing what you expect.
> it did so in the past, but there was never any guarantee that this
> work, and evidently it no longer does.
>> Balasubramanian Ganesan
>> Research Assistant Professor
>> Center for Integrated BioSystems
>> Utah State University
>> 4700 Old Main Hill
>> Logan UT 84322
>> balag at cc.usu.edu
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> James W. MacDonald, M.S.
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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