[BioC] Affxparser: warning creating cel file from AffyBatch

[Hooiveld, Guido]

Thanks, I got it. I wasn't aware of the difference between 'file' and
'package'.

Working fine now (solution 2).

Guido


 

> -----Original Message-----
> From: kasperdanielhansen at gmail.com 
> [mailto:kasperdanielhansen at gmail.com] On Behalf Of Kasper 
> Daniel Hansen
> Sent: 22 February 2010 22:33
> To: Hooiveld, Guido
> Subject: Re: Affxparser: warning creating cel file from AffyBatch
> 
> I would say the _warning_ (which is not an error) is pretty 
> clear: you do not have a CDF file for this chip type in your 
> path (note the difference between CDF file (from affy) and 
> CDF package (from Bioc)).
> If that is available, some extra checking of the created CEL 
> file against the supplied CDF file is performed.
> 
> You can therefore either
> 1) ignore it, it is only a warning after all
> 2) supply a CDF file in the "path", for example in the same 
> directory as you create the CEL files.
> 
> Kasper
> 
 

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Hooiveld, Guido
> Sent: 18 February 2010 22:20
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Affxparser: warning creating cel file from AffyBatch
> 
> 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         
> > 
>  
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> 
> ------------------------------------------------
> 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 at wur.nl 
> 
> 
> 
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