[BioC] Why is my matrix transposed?

[Kasper Daniel Hansen]

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  
underlying representation.

Kasper

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.
>>
>>> 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.
>
> You get this discrepancy because write.table() isn't designed to use  
> an
> S4 object. From ?write.table
>
> Arguments:
>
>        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  
> written
> to do what you want, you are assuming that the coercion of an
> ExpressionSet to data.frame will end up doing what you expect.  
> Evidently
> it did so in the past, but there was never any guarantee that this  
> would
> work, and evidently it no longer does.
>
> Best,
>
> Jim
>
>
>>
>> Balasubramanian Ganesan
>> Research Assistant Professor
>> Center for Integrated BioSystems
>> Utah State University
>> 4700 Old Main Hill
>> Logan UT 84322
>> balag at cc.usu.edu
>>
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>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
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