Dear list,
 
I am using Affxparser to create/save CEL files from an AffyBatch object.
The code I use used to work fine before 2 yrs ago, but now I get a
warning. Although the corresponding CDF file is installed, and the new
CEL file is properly created, I would appreciate getting feedback how to
avoid this warning. Code below.
 
Thanks,
Guido
 
> library(affxparser)
> library(affy)
Loading required package: Biobase
 
Welcome to Bioconductor
 
  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.
 
Warning message:
package 'affy' was built under R version 2.9.1 
> affy.data <- ReadAffy()
> affy.data
AffyBatch object
size of arrays=712x712 features (11 kb)
cdf=ATH1-121501 (22810 affyids)
number of samples=24
number of genes=22810
annotation=ath1121501
notes=
>  
> prefix <- "Guido"
> 
> #get the intensity
> size = ncol(affy.data)
> IN = intensity(affy.data)
> 
> #get the celfile names
> cels = colnames(IN)
> #put the prefix to the celfile names
> newcels = paste(prefix,cels,sep="-")
> #get the number of chips
> col.count = dim(IN)[2]
> #go through each chip and write the new celfile for it
> for( i in 1:col.count){
+ #old celfile name for this chip
+ file.name = cels[i]
+ #new celfile name for this chip
+ file.name2 = newcels[i]
+ INi <- IN[,i];
+ INi[is.na(INi)] = 1000000000;
+ meg = paste("handling file:",file.name)
+ print (meg)
+ 
+ # Read the CEL header
+ HDRi <- readCelHeader(file.name)
+                 HDRi$chiptype <- cleancdfname(HDRi$chiptype,
addcdf=FALSE)
+ 
+ # Create a CEL v4 file of the same chip type
+ outFile <- file.path(as.character(file.name2))
+ if (file.exists(outFile))
+   file.remove(outFile)
+ createCel(outFile, HDRi, overwrite=TRUE)
+ 
+ # Update the newly created CEL file by injecting corrected values
+ updateCel(outFile, indices=NULL, intensities=INi)
+ }
[1] "handling file: A175_11_WT.CEL"
[1] "handling file: A175_12_WT.CEL"
[1] "handling file: A175_13_WT.CEL"
[1] "handling file: A175_21_S036.CEL"
<SNIP>
[1] "handling file: A175_82_OXS042.CEL"
[1] "handling file: A175_83_OXS042.CEL"
There were 24 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In createCel(outFile, HDRi, overwrite = TRUE) :
  Skipping validation of CEL header against CDF header. Could not find a
CDF file for this chip type: ath1121501
2: In createCel(outFile, HDRi, overwrite = TRUE) :
  Skipping validation of CEL header against CDF header. Could not find a
CDF file for this chip type: ath1121501
3: In createCel(outFile, HDRi, overwrite = TRUE) :
  Skipping validation of CEL header against CDF header. Could not find a
CDF file for this chip type: ath1121501
4: In createCel(outFile, HDRi, overwrite = TRUE) :
  Skipping validation of CEL header against CDF header. Could not find a
CDF file for this chip type: ath1121501
<AND 20 additional, identical warnings)
 
 
> sessionInfo()
R version 2.9.0 (2009-04-17) 
i386-pc-mingw32 
 
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
 
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

 
other attached packages:
[1] ath1121501cdf_2.4.0 affy_1.22.1         Biobase_2.4.1
affxparser_1.16.0  
 
loaded via a namespace (and not attached):
[1] affyio_1.12.0        preprocessCore_1.6.0 tools_2.9.0         
> 
 
 
 
 
 
 
 
 
 
 
 
 
 

------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
email:      guido.hooiveld@wur.nl 



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