[BioC] split.AffyBatch

James MacDonald jmacdon at med.umich.edu
Wed Jul 21 20:37:06 CEST 2004

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).

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

first.abatch <- abatch[,c(1,3,5)]
second.abatch <- abatch[,c(2,4,6,7,8,9)]



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> 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? 




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