[BioC] Re: affycomp: info.txt is Ok, new error message

[Mohammad Esad-Djou]

"Harris A. Jaffee" <hjaffee at jhmi.edu> schrieb am 24.05.05 16:29:56: 
> You seem to have submitted 3 identical hgu133 files (with the methods
> specified differently).  They were all assessed successfully, as you
> can see in the table:
> 
>    http://affycomp.biostat.jhsph.edu/AFFY2/TABLES.hgu/0.html#table133

yes.  They are correct. 

> I don't know why your 4th submission failed assessment:

I wanted to use my csv file instead of hgu133.csv (as standard example). I assume that I does not produce my csv file correctly.
I cannot understand, where the problem lies. I use the following instructions:

library(affy)
library(tools)
library(affycomp)

# 42 Experiment
data.raw <- ReadAffy(filenames=	"./R/ME_cel/Expt1_R1.CEL",
...		
		"./R/ME_cel/Expt1_R2.CEL",
				"./R/ME_cel/Expt14_R3.CEL")

my.Data <- expresso(data.raw, bg.correct = F, normalize = F, pmcorrect.method = "pmonly", summary.method = "medianpolish")
x <-  exprs(my.Data)
write.table(data.frame(x,check.names=FALSE),file="./R/excel/ME_133_1.csv",sep=",",col.names=NA,quote=FALSE) 

and then I receive in affycomp.R for ME_133_1.csv as my example:
> Error in "[.data.frame"(s, , rownames(pData(pd))) :
> undefined columns selected
> Execution halted

How can I produce correct csv file from CEL files? 

> Can I remove some/all of the duplication?
Yes, please. I wanted to ask from you about it.

best regards,
Mohammad