[BioC] affycomp and data.frame

[Mohammad Esad-Djou]

Thanks for your answer.  

I have the following questions:

1.  How can I produce data.frame correct without Preprocessing (MAS5, RMA, liwong...)?  
I know that the instruction is not correct:

 data.raw <- ReadAffy(filenames="./R/ME_cel/Expt1_R1.CEL",
                                                  ...
 			"./R/ME_cel/Expt7_R2.CEL")
x<- exprs(data.raw)

but I have unfortunately no new Idea! 

2. (in affycomp) Can I use directly *.CEL files instead of *.csv? If yes, how?


Thanks,
Mohmmad Esad-Djou

"Rafael A. Irizarry" <ririzarr at jhsph.edu> schrieb am 18.05.05 20:35:36:
> 
> the instructions say you should do this:
> 
> x <- exprs(eset)
> write.table(data.frame(x,check.names=FALSE),file="filename.csv",sep=",",col.names=NA,quote=FALSE)  
> 
> 
> -r
> 
> On Wed, 18 
> May 2005, Mohammad Esad-Djou wrote:
> 
> > Hello,
> > 
> > I try through affycomp different methods with one another compare.
> > 
> > I have step by step instructions of http://affycomp.biostat.jhsph.edu/#whatisthis used:
> > 
> > >>Data and instructions 
> > >>Download the spike-in and dilution data sets. 
> > 
> > >>Spike-in hgu133a Data 
> > >>Affymetrix's Spike-in hgu133a Experiment CEL files [gzip-compressed tar-archive] 
> > 
> > >>Description file for this data [text] 
> > 
> > ::: I downloaded.
> > 
> > >>2. Obtain expression measures (in original scale, NOT log scale) for any or all of the datasets, and write each as a comma-delimited text file as follows: 
> > >>For R users, if x is matrix with probe set IDs as rownames and filenames as colnames, the command write.table(data.frame(x,check.names=FALSE),file="filename.csv",sep=",",col.names=NA,quote=FALSE) should do the trick. 
> > >>For convenience, we offer two example files [compressed archive] in the correct format, one for dilution and one for spike-in. 
> > 
> > ::: Iwrote:
> > 
> > library(affy)
> > library(affycomp)
> > 
> > data.raw <- ReadAffy(filenames="./R/ME_cel/Expt1_R1.CEL",
> >                                                  ...
> > 			"./R/ME_cel/Expt7_R2.CEL")
> > 
> > eset <- mas5(data.raw)
> > 
> > :::For data.frame I receive error message:
> > #write.table(eset(x,check.names=FALSE),file="filename.csv",sep=",",col.names=NA,quote=FALSE)
> > #Error in inherits(x, "data.frame") : couldn't find function "eset"
> > 
> > ::: I can the following commands use, but csv file is not stored like given examples: 
> > write.table(eset,file="filename.csv",sep=",",col.names=NA,quote=FALSE)
> > 
> > How can I produce correct data.frame?
> > 
> > Thanks,
> > Mohammad Esad-Djou
> > 
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