Question: Affxparser: warning creating cel file from AffyBatch
0
gravatar for Guido Hooiveld
9.5 years ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:
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@wur.nl [[alternative HTML version deleted]]
cdf affy affxparser • 643 views
ADD COMMENTlink modified 9.5 years ago • written 9.5 years ago by Guido Hooiveld2.5k
Answer: Affxparser: warning creating cel file from AffyBatch
0
gravatar for Guido Hooiveld
9.5 years ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:
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 <- 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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENTlink written 9.5 years ago by Guido Hooiveld2.5k
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 >> >> >> >> ? ? ? [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 9.5 years ago by Henrik Bengtsson2.4k
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