[BioC] problems with affy in unix

[Naomi Altman]

Thanks for all of the information.  I was also faced with not enough 
memory, but was able to obtain expression values using justRMA.  From the 
documentation, it looks like this is what I want for normalization, but I 
am not sure how the expression values are derived from the normalized probes.

This is the set of expresso options I would have used:

expression=expresso(data,bgcorrect.method="rma",normalize.method="quantiles",
pmcorrect.method="pmonly",summary.method="liwong")


Thanks,
Naomi Altman


At 10:29 AM 7/19/2003 -0400, James MacDonald wrote:
>1. You don't have enough memory to merge the two. 335 cel files will
>take a TON of memory to deal with.
>
>2. No idea on this one. What are the names of the cel files?
>
>3. If you are just going to do RMA, then you could use justRMA instead.
>You may have enough memory to do it, because this function is much less
>memory intensive.
>
>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
>
> >>> "feiwan" <wanf at email.uc.edu> 07/18/03 11:41PM >>>
>Dear bioconductor users:
>
>I encontoured two problems with affy in unix. the dataset is the
>Leukemia data from Stjude.org
>
>Question1:
>
>I tried to merge two big affybatch data sets in R (under unix
>mainframe) and encounter the problems as following:
>
>combine2.3<-merge(combine2.1,TALL)
>Error: cannot allocate vector of size 409600 Kb
>
>Question2:
>
>Affybatch BCR does not have names for each sample (only H).
>
> > > > setwd("/export/home/fwan/data/BCR")
>BCR<-ReadAffy()>
> > BCR
>AffyBatch object
>size of arrays=640x640 features (51204 kb)
>cdf=HG_U95Av2 (12625 affyids)
>number of samples=16
>number of genes=12625
>annotation=hgu95av2
> > exprs(BCR)[1,]
>    H    H    H    H    H    H    H    H    H    H    H    H    H    H
>  H    H
>  687  859  883  608  711  567  827  572  621  607  565  802 1292  583
>683  659
> >
>
>Question3:
>
>there 335 cel files and If R can not process all of them at the same
>time, can I break them into different groups and then run RMA on each
>group? I know the final expression values will be different but I do not
>know if it will have a big effects on final data analysis.
>
>
>
>I am very new to this area. any suggustion will be appreciated.
>
>regards,
>
>w.f
>
>
>
>
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>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111