the whole R source code shoud be:
  >raw.data <- read.exon()
> raw.data@cdfName <- "exon.pmcdf"
> x.rma <- rma(raw.data)
> write.table(x.rma, file="x.csv", sep="\t")

  the generated file x.csv has 1,411,190 conlumns titles "x231501" "X2315102"....
  can you please answer the following questions?
  1. how to find relation bewteen probset and probes in exonmap library?
  2. is it possible to find normalized value for each probe value ?
   
  
> can you please tell me what the meaning of columns? are they
> expression levels for all probesets?
> how can i get RMA expression level  for each probe?


Kasper Daniel Hansen <khansen@stat.Berkeley.EDU> wrote:
  
On Jan 17, 2008, at 4:57 PM, Jay an wrote:

> Thanks Martin and James,
>
> after doing write.table(x.rma, file="x.csv", sep="\t")
> the file x.csv has 1,411,190 conlumns titles "x231501" "X2315102"....
> can you please tell me what the meaning of columns? are they
> expression levels for all probesets?
> how can i get RMA expression level for each probe?

What do you mean by this. Typically summarization is considered part 
of the RMA method and after summarization you have probeset level 
values, not probe level values.

Kasper


>
> Yuan
>
>
> Martin Morgan wrote:
> "James W. MacDonald" writes:
>
>> Hi Yuan,
>>
>> Jay an wrote:
>>> Hello,
>>> I got several .CEL files to do RMA using exonmap library below:
>>>> raw.data <- read.exon()
>>>> raw.data@cdfName <- "exon.pmcdf"
>>>> x.rma <- rma(raw.data)
>>>> write.table(x.rma, file="x.csv", sep="\t")
>>
>> I'm surprised that worked. If you want to write out the expression
>
> There's a method that converts an ExpressionSet into a data.frame,
> taking the transpose of the expression values and cbind'ing (adding as
> columns) the phenotypic data.
>
>> library(Biobase)
>> data(sample.ExpressionSet)
>> names(as(sample.ExpressionSet, "data.frame"))
> [1] "AFFX.MurIL2_at" "AFFX.MurIL10_at"
> [3] "AFFX.MurIL4_at" "AFFX.MurFAS_at"
> [5] "AFFX.BioB.5_at" "AFFX.BioB.M_at"
> ...
> [499] "X31738_at" "X31739_at"
> [501] "sex" "type"
> [503] "score"
>
> This gets invoked by write.table and other functions that try to
> coerce their arguments to a data.frame. This can be convenient for
> instance in machine learning, where you can write a formula with '.'
> to indicate 'all columns' of a data.frame, and just provide the
> (probably filtered) ExpressionSet as the data argument.
>
> The affyPLM package might help to 'get RMA expression levels for each
> probe'.
>
> Martin
>
>> values you want to use write.exprs(), not write.table(), which is
>> intended to write out data.frames or matrices (and x.rma is neither).
>>
>> Best,
>>
>> Jim
>>
>>
>>> the file x.csv has 1,411,190 conlumns titles "x231501" 
>>> "X2315102"....
>>> can you please tell me what the meaning of columns? are they
>>> expression levels for all probesets?
>>> how can i get RMA expression level for each probe?
>>>
>>>
>>> thanks
>>> Yuan
>>>
>>>
>>>
>>>
>>> ---------------------------------
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>> gmane.science.biology.informatics.conductor
>>
>> -- 
>> James W. MacDonald, M.S.
>> Biostatistician
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/ 
>> gmane.science.biology.informatics.conductor
>
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>
>
>
> ---------------------------------
>
>
> ---------------------------------
>
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>
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> gmane.science.biology.informatics.conductor



       
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