[BioC] affy: expresso in separated steps

[cstrato]

Dear Kenji,

Please have a look at the help file "?export" which shows you how to 
save the results as text files.
If you set parameter "as.dataframe=TRUE" the text file will be 
automatically imported into R as data.frame.

Best regards
Christian


Leonardo K. Shikida wrote:
> Hi Christian
>
> this seems to be in the right direction, but I could not find any
> example of how it explicitly saves intermediary results as text files
>
> thanks in advance
>
> Kenji
>
>
>
> On Thu, Oct 15, 2009 at 6:22 PM, cstrato <cstrato at aon.at> wrote:
>   
>> Dear Kenji,
>>
>> Maybe you could use package xps, which has a similar function "express"
>> which allows you to do normalization stepwise and save interim results as
>> text files for reuse, see e.g. the recent vignette:
>> http://bioconductor.org/packages/2.5/bioc/vignettes/xps/inst/doc/xpsPreprocess.pdf
>> and the script in xps/examples/script4xpsPreprocess.R
>>
>> Best regards
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>> V.i.e.n.n.a           A.u.s.t.r.i.a
>> e.m.a.i.l:        cstrato at aon.at
>> _._._._._._._._._._._._._._._._._._
>>
>>
>> Leonardo K. Shikida wrote:
>>     
>>> Hi James
>>>
>>> thanks for the fast answer
>>>
>>> I am afraid I can't do that. The idea here is to reuse some other
>>> normalization methods (not implemented in R), so I'd have to, somehow,
>>> save these intermediary results, perform another normalization method,
>>> then restore this normalized data to perform summarization, etc
>>>
>>> The problem, as you've pointed out, is that affy abstracts the
>>> internal data structure to make my life easier. My work will probably
>>> need to deal with this internal structure somehow.
>>>
>>> Maybe I could just save the object, export PM and MM data as CSV,
>>> perform the normalization, then restore the object using the load
>>> command and overwrite its PM and MM data with the normalized CSV
>>> files...
>>>
>>> Sounds like an horrible way to deal with this situation :-) so I am
>>> open to better ideas...
>>>
>>> []
>>>
>>> Kenji
>>>
>>>
>>>
>>> On Thu, Oct 15, 2009 at 5:00 PM, James W. MacDonald
>>> <jmacdon at med.umich.edu> wrote:
>>>
>>>       
>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>>           
>>>> --
>>>> 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
>>>>
>>>>
>>>>         
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>>       
>>     
>
>