[BioC] exonmap RMA function

Martin Morgan mtmorgan at fhcrc.org
Thu Jan 17 18:45:36 CET 2008


"James W. MacDonald" <jmacdon at med.umich.edu> 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 at 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
>>    
>>    
>> 
>>        
>> ---------------------------------
>> 
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>> 
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>
> -- 
> 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
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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