[BioC] problems with affy in unix

[Rafael A. Irizarry]

On Mon, 21 Jul 2003, Naomi Altman wrote:

> 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")
> 

this is not what justRMA gives you. justRMA is equivalent to

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

so medianpolish, instead of 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
> >
> >
> >
> >
> >         [[alternative HTML version deleted]]
> >
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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
> 
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