[BioC] Affxparser: warning creating cel file from AffyBatch

Tue Feb 23 12:10:37 CET 2010

On Tue, Feb 23, 2010 at 10:54 AM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> Thanks, I got it. I wasn't aware of the difference between 'file' and
> 'package'.

You're not the first one.  This is a very common misunderstanding and
introduce lots of unnecessary confusion;

  http://aroma-project.org/definitions/chipTypesAndCDFs

It's not uncommon that BioC users/developers say "the CDF" when they
really mean "the CDF package", especially when talking about "custom
CDFs".

Another $.02 of mine

/Henrik

>
> 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
>> >
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------
>> 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
>>
>>
>>
>>       [[alternative HTML version deleted]]
>>
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