[BioC] affy: expresso in separated steps

[James W. MacDonald]

Hi Kenji,

Leonardo K. Shikida wrote:
> Hi
> 
> I'd like to know how to perform affy expresso in separate steps
> 
> for example
> 
> what I'd like is
> 
> CEL data => bg correction => save corrected data into a file X
> load file X => normalization => save normalized data into file Y
> load file Y => summarization => save summarized data into file Z

I wouldn't save things in files. The objects designed to contain your 
data are pretty complex, but are designed to make manipulation of your 
data simple. If you write out to files you increase the complexity of 
dealing with your data and lose all of the nice functions designed to 
make your life simpler.

You can instead keep your data in an AffyBatch (until you summarize) and 
just save the objects as you go through your process. For instance:

dat <- ReadAffy()
bgdat <- bg.correct(dat, method)

## for methods see bgcorrect.methods()

normdat <- normalize(bgdat, method)

## for methods see normalize.methods(dat)

eset <- computeExprSet(normdat, summary.method = method, 
pmcorrect.method = pmmethod)

## for summary and pmcorrect methods see
express.summary.stat.methods()
pmcorrect.methods()


> 
> and so on
> 
> it's not clear to me
> 
> [1] how to access these intermediary datasets. should I save both
> pm(Data) and mm(Data)?
> [2] if the only thing I need is the intermediary dataset or if I need
> anything alse such as platform info (CDF files for example)

You will need a cdf package. If you are using a commercially available 
chip and just want to use the 'regular' Affy cdf, then you don't need to 
do anything. If you don't have the required package it will be 
downloaded for you. If you want to use a different cdf, there is the 
cdfname argument to ReadAffy (if BioC has these cdfs; an example would 
be the MBNI cdfs). If the chip isn't commercial, you will need to get 
the cdf from Affy, build a package using the makecdfenv package, and 
then build and install yourself.

Best,

Jim


> 
> I hope I've been clear about my doubt
> 
> thanks in advance
> 
> Kenji
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826