Dear all,
I am learning to analyse Affymetrix microarray data but I have a problem in reading .cel files in. 
I downloaded from GEO the raw data provided as supplementary files (GSE12345_RAW.tar), than I have extracted the cel files in a directory which I have set as my working directory.
Here is the R code I used:

> setwd("C:/BACKUP/Dati/Progetti/Landi/meta-analisi MPM/GSE12345_RAW")
> library(affy)
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> dir()
 [1] "data analysis.txt"     "E-GEOD-12345.sdrf.txt" "E-GEOD-12345.sdrf.xls"
 [4] "GSM309986.CEL"         "GSM309987.CEL"         "GSM309988.CEL"        
 [7] "GSM309989.CEL"         "GSM309990.CEL"         "GSM309991.CEL"        
[10] "GSM310012.CEL"         "GSM310013.CEL"         "GSM310014.CEL"        
[13] "GSM310015.CEL"         "GSM310016.CEL"         "GSM310068.CEL"        
[16] "GSM310070.CEL"         "target.txt"            "target.xls"           
> pd <- read.AnnotatedDataFrame("target.txt",header=TRUE,row.names=1,as.is=TRUE)
> pData(pd)
         FileName              Target
N1  GSM309986.CEL      pleural tissue
N2  GSM309987.CEL      pleural tissue
N3  GSM309988.CEL      pleural tissue
N4  GSM309989.CEL      pleural tissue
MM1 GSM309990.CEL mesothelioma tissue
MM2 GSM309991.CEL mesothelioma tissue
MM3 GSM310012.CEL mesothelioma tissue
MM4 GSM310013.CEL mesothelioma tissue
MM5 GSM310014.CEL mesothelioma tissue
MM6 GSM310015.CEL mesothelioma tissue
MM7 GSM310016.CEL mesothelioma tissue
MM8 GSM310068.CEL mesothelioma tissue
MM9 GSM310070.CEL mesothelioma tissue
> rawData <- read.affybatch(filenames=pData(pd)$FileName,phenoData=pd)
Error in try(.Call("ReadHeaderDetailed", filename, PACKAGE = "affyio")) : 
  Is GSM310016.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats.

Errore in read.celfile.header(filenames[i], info = "full") : 
  Failed to get full header information for GSM310016.CEL
> rawData1<-ReadAffy()
Error in try(.Call("ReadHeaderDetailed", filename, PACKAGE = "affyio")) : 
  Is C:/BACKUP/Dati/Progetti/Landi/meta-analisi MPM/GSE12345_RAW/GSM310016.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats.

Errore in read.celfile.header(filenames[i], info = "full") : 
  Failed to get full header information for C:/BACKUP/Dati/Progetti/Landi/meta-analisi MPM/GSE12345_RAW/GSM310016.CEL
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252   
[3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C                  
[5] LC_TIME=Italian_Italy.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] affy_1.32.1    Biobase_2.14.0

loaded via a namespace (and not attached):
[1] affyio_1.22.0         BiocInstaller_1.2.1   preprocessCore_1.16.0
[4] zlibbioc_1.0.0       
> traceback()
7: stop("Failed to get full header information for ", filename)
6: read.celfile.header(filenames[i], info = "full")
5: FUN(1:13[[11L]], ...)
4: lapply(X = X, FUN = FUN, ...)
3: sapply(seq_len(length(filenames)), function(i) {
       sdate <- read.celfile.header(filenames[i], info = "full")[["ScanDate"]]
       if (is.null(sdate) || length(sdate) == 0) 
           NA_character_
       else sdate
   })
2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, 
       description = l$description, notes = notes, compress = compress, 
       rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, 
       verbose = verbose, sd = sd, cdfname = cdfname)
1: ReadAffy()

May be there is a problem in reading the cel file header, so I opened one of the cel files with a text-editor but it seems correct.
Can anyone help me?
Thank you very much!
Manuela

----------------------------------------------------------------------------------------
Manuela Di Russo, Ph.D. Student
Department of Experimental Pathology, MBIE
University of Pisa
Pisa, Italy
e-mail: manuela.dirusso@for.unipi.it
tel: +39050993538
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