[BioC] split.AffyBatch

[Laurent Gautier]

James MacDonald wrote:
> split.AffyBatch() is not designed to split AffyBatches in the manner you
> want. Instead, it is designed to split on rows, based on a certain
> factor (e.g., it is working as designed).

I think I designed split.AffyBatch to split on columns (and 
'example(split.AffyBatch)'
seems to confirm that).

Splitting on rows does not make much sense unless you update the cdfenv 
at the same time because of the indexing system (this is already 
implemented and under testing... it will go public

On my machine it seems to work fine with the example (R-1.9.1, 
affy-1.5.1) and I cannot see what Wen-Bin refers to. For help, more 
information (like the version number for R and for the package, and the 
exact function call used.) would be needed.



> If you want to split your AffyBatch by columns, you simply subset. For
> instance, to split into two AffyBatches where one contains the first
> three columns and the other the last six,
> 
> first.abatch <- abatch[,1:3]
> second.abatch <- abatch[,4:9]
> 
> If you want non-contiguous columns, you simply concatenate the column
> numbers.
> 
> first.abatch <- abatch[,c(1,3,5)]
> second.abatch <- abatch[,c(2,4,6,7,8,9)]
> 
> HTH,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> 
>>>>Wenbin Liu <snakeeye1966 at yahoo.com> 07/21/04 01:07PM >>>
> 
> Dear all, 
> 
> I was using affy package's split.AffyBatch function to
> split an AffyBatch (9 affy chips with 45101
> probesets/chip) to two parts, expecting 3 columns for
> the exprSet of one part and 6 for the the other, with
> 45101 rows for both. However, it divided the rows
> instead of columns. 
> 
> I updated the package affy, but it didn't help.
> 
> Has someone encountered a similar problem? 
> 
> Thanks,
> 
> Wenbin
> 
> 
> 
> 
> 	
> 		
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