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 <- readCelHeaderfile.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 >> >> >> >> ? ? ? 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