[BioC] getting MAS for a large affy object

[James MacDonald]

With MAS5, you don't have to analyze all of your data at the same time
(unlike most of the other methods in the affy package), so really all
you need to do is combine the data based on tissue origin.

It is simple to combine the data if you know which samples are a
particular tissue type. Use the exprs() accessor function to extract the
required columns from each of your exprSets. For instance, if you have
three exprSets and the first five columns in each are a given tissue,
you can combine into a matrix like this:

first.tissue <- cbind(exprs(exprSet.one)[,1:5],
exprs(exprSet.two)[,1:5], exprs(exprSet.three)[,1:5])

Where exprSet.one, etc are the names of your exprSets.

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
>>> Hao Liu <liuha at umdnj.edu> 04/24/04 10:20 PM >>>
Dear All:

I read 178 affy results into on object using ReadAffy().

however, when I tried to computer MAS, the computer apparently don't
have enough memory to complete the operation. I wonder if there is
anyway
to circumvent this.

Another question is after getting MAS, how do I write results to
different
file based on the origin of the tissue?

I have all affy in MAS5 but in separate files, I wonder if I can use R
to
combine them based on their tissue origin, this is actually an
alternative
to what I asked above -- but I am no good with R.

Best regards

Hao Liu, Ph. D

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