Question: Making a PD package for Oligo
0
gravatar for Colleen Doherty
12.2 years ago by
Colleen Doherty40 wrote:
Hi, I am having some problems making a PD package for the Arabidopsis ATH1 expression chip so that I can switch to using Oligo. I initially tried to use pdInfoBuilder: pkg<-new("AffySNPPDInfoPkgSeed", email = "dohert23 at msu.edu", cdfFile = cdfFile, csvAnnoFile = csvAnno, csvSeqFile = csvSeq) but this was unsuccessful -it just creates an empty file with no warnings. Trying to make a package with that gives this: makePdInfoPackage(pkg, destDir=".")Creating package in ./pd.ath1.121501 Error in gsub(nm[i], symbolValues[[i]], res) : invalid argument possibly because I was using the wrong class since this is not an SNP chip? So I switched to the makePlatformDesign package and got this: makePDpackage("ATH1-121501.CDF", file1=csvSeq, file2= csvAnno, manufacturer="affymetrix", type="expression") affymetrix expression The package will be called pd.ath1.121501 Reading CDF File Error in read.cdffile.list(filename) : SET_STRING_ELT() can only be applied to a 'character vector', not a 'list' I searched the mailing list and found a similar error: makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap",file1="Mm_PromPR_v02.cif", manufacturer="affymetrix", type="tiling") > affymetrix tiling > The package will be called pd.mm.prompr.v01.ncbiv35 > Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : > SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL' but it looks like this was a windows specific error that was solved by upgrading and I think have updated everything (sessionInfo below). So I am guessing that my error is that my files are entered incorrectly or something (they are all in the working directory) I know Benilton (and probably many others) have already made this for the ATH1 chip, so obtaining a copy of that would be a short term fix, but I would also like to know what I am doing incorrectly in either (or both) packages. Thanks, Colleen sessionInfo below: R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] makePlatformDesign_1.2.0 affyio_1.4.1 oligo_1.2.0 [4] oligoClasses_0.99.5 affxparser_1.9.5 AnnotationDbi_0.99.24 [7] preprocessCore_0.99.22 RSQLite_0.6-3 DBI_0.2-3 [10] Biobase_1.14.1 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 -- Colleen Doherty Thomashow Lab 310 Plant Biology Michigan State University East Lansing, MI 48824
cdf oligo makeplatformdesign • 569 views
ADD COMMENTlink modified 12.2 years ago by Benilton Carvalho4.3k • written 12.2 years ago by Colleen Doherty40
Answer: Making a PD package for Oligo
0
gravatar for Benilton Carvalho
12.2 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
Hi Colleen, the pdInfoBuilder will not work just yet... In the (near, I hope) future, pdInfoBuilder should handle everything, but for the moment only SNP arrays are supported. So, you're on the right track, use makePlatformDesign. I do remember seeing errors like the one you reported and I think upgrading the affyio package will fix it. Give that a try and let us know what your sessionInfo() is, okay? best, b On Oct 4, 2007, at 1:41 PM, Colleen Doherty wrote: > Hi, > > I am having some problems making a PD package for the Arabidopsis ATH1 > expression chip so that I can switch to using Oligo. > I initially tried to use pdInfoBuilder: > > pkg<-new("AffySNPPDInfoPkgSeed", email = "dohert23 at msu.edu", cdfFile > = cdfFile, csvAnnoFile = csvAnno, csvSeqFile = csvSeq) > but this was unsuccessful -it just creates an empty file with no > warnings. > > Trying to make a package with that gives this: > makePdInfoPackage(pkg, destDir=".")Creating package in ./ > pd.ath1.121501 > Error in gsub(nm[i], symbolValues[[i]], res) : invalid argument > > possibly because I was using the wrong class since this is not an > SNP chip? > > So I switched to the makePlatformDesign package and got this: > > makePDpackage("ATH1-121501.CDF", file1=csvSeq, file2= csvAnno, > manufacturer="affymetrix", type="expression") > affymetrix expression > The package will be called pd.ath1.121501 > Reading CDF File > Error in read.cdffile.list(filename) : > SET_STRING_ELT() can only be applied to a 'character vector', not > a 'list' > > I searched the mailing list and found a similar error: > > makePDpackage > ("Mm_PromPR_v01_NCBIv35.bpmap",file1="Mm_PromPR_v02.cif",manufacturer= > "affymetrix", > type="tiling") >> affymetrix tiling >> The package will be called pd.mm.prompr.v01.ncbiv35 >> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : >> SET_VECTOR_ELT() can only be applied to a 'list', not a >> 'NULL' > > but it looks like this was a windows specific error that was solved by > upgrading and I think have updated everything (sessionInfo below). So > I am guessing that my error is that my files are entered incorrectly > or something (they are all in the working directory) > > I know Benilton (and probably many others) have already made this for > the ATH1 chip, so obtaining a copy of that would be a short term fix, > but I would also like to know what I am doing incorrectly in either > (or both) packages. > > Thanks, > Colleen > > > sessionInfo below: > > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US > .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. > UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 > ;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets > [8] methods base > > other attached packages: > [1] makePlatformDesign_1.2.0 affyio_1.4.1 oligo_1.2.0 > [4] oligoClasses_0.99.5 affxparser_1.9.5 > AnnotationDbi_0.99.24 > [7] preprocessCore_0.99.22 RSQLite_0.6-3 DBI_0.2-3 > [10] Biobase_1.14.1 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-15 > > -- > Colleen Doherty > Thomashow Lab > 310 Plant Biology > Michigan State University > East Lansing, MI 48824 > > _______________________________________________ > 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 12.2 years ago by Benilton Carvalho4.3k
Hi Benilton, Thanks! Updating affyio fixed the original reason I was trying to make a new PDpackage in the first place. Previously, when using read.celfiles in oligo I was getting this error: Error in .nextMethod(e1, e2) updating affyio fixed that and I can now use read.celfiles with the old pd.ath1.121510 I guess I don't need a new PDpackage now, but I still have a problem making one- if the mistake is obvious to anyone I would appreciate some advice. > cdf<-"ATH1-121501.CDF" > csv<-"ATH1-121501.na23.annot.csv" > probe<-"ATH1-121501_probe_tab" > makePDpackage(cdf,file1=csv, file2=probe, manufacturer="affymetrix", type="expression") affymetrix expression The package will be called pd.ath1.121501 Reading CDF File Reading Sequence Info Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 6 elements > sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] makePlatformDesign_1.2.0 affyio_1.6.0 oligo_1.2.0 [4] oligoClasses_1.0.0 affxparser_1.10.0 AnnotationDbi_1.0.0 [7] preprocessCore_1.0.0 RSQLite_0.6-3 DBI_0.2-3 [10] Biobase_1.16.0 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 > Thanks, Colleen
ADD REPLYlink written 12.2 years ago by Colleen Doherty40
Duh! I switched file1 and file2- works great now- THANKS! On 10/5/07, Colleen Doherty <colleen.doherty at="" gmail.com=""> wrote: > Hi Benilton, > > Thanks! Updating affyio fixed the original reason I was trying to > make a new PDpackage in the first place. > > Previously, when using read.celfiles in oligo I was getting this error: > Error in .nextMethod(e1, e2) > updating affyio fixed that and I can now use read.celfiles with the > old pd.ath1.121510 > > I guess I don't need a new PDpackage now, but I still have a problem > making one- if the mistake is obvious to anyone I would appreciate > some advice. > > > > cdf<-"ATH1-121501.CDF" > > csv<-"ATH1-121501.na23.annot.csv" > > probe<-"ATH1-121501_probe_tab" > > makePDpackage(cdf,file1=csv, file2=probe, manufacturer="affymetrix", type="expression") > affymetrix expression > The package will be called pd.ath1.121501 > Reading CDF File > Reading Sequence Info > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > line 1 did not have 6 elements > > > sessionInfo() > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] makePlatformDesign_1.2.0 affyio_1.6.0 oligo_1.2.0 > [4] oligoClasses_1.0.0 affxparser_1.10.0 AnnotationDbi_1.0.0 > [7] preprocessCore_1.0.0 RSQLite_0.6-3 DBI_0.2-3 > [10] Biobase_1.16.0 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-15 > > > > Thanks, > Colleen > -- Colleen Doherty Thomashow Lab 310 Plant Biology Michigan State University East Lansing, MI 48824
ADD REPLYlink written 12.2 years ago by Colleen Doherty40
In that case ignore the message I just sent ;-D Jim Colleen Doherty wrote: > Duh! I switched file1 and file2- works great now- > THANKS! > > On 10/5/07, Colleen Doherty <colleen.doherty at="" gmail.com=""> wrote: >> Hi Benilton, >> >> Thanks! Updating affyio fixed the original reason I was trying to >> make a new PDpackage in the first place. >> >> Previously, when using read.celfiles in oligo I was getting this error: >> Error in .nextMethod(e1, e2) >> updating affyio fixed that and I can now use read.celfiles with the >> old pd.ath1.121510 >> >> I guess I don't need a new PDpackage now, but I still have a problem >> making one- if the mistake is obvious to anyone I would appreciate >> some advice. >> >> >>> cdf<-"ATH1-121501.CDF" >>> csv<-"ATH1-121501.na23.annot.csv" >>> probe<-"ATH1-121501_probe_tab" >>> makePDpackage(cdf,file1=csv, file2=probe, manufacturer="affymetrix", type="expression") >> affymetrix expression >> The package will be called pd.ath1.121501 >> Reading CDF File >> Reading Sequence Info >> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : >> line 1 did not have 6 elements >> >>> sessionInfo() >> R version 2.6.0 (2007-10-03) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] makePlatformDesign_1.2.0 affyio_1.6.0 oligo_1.2.0 >> [4] oligoClasses_1.0.0 affxparser_1.10.0 AnnotationDbi_1.0.0 >> [7] preprocessCore_1.0.0 RSQLite_0.6-3 DBI_0.2-3 >> [10] Biobase_1.16.0 >> >> loaded via a namespace (and not attached): >> [1] rcompgen_0.1-15 >> Thanks, >> Colleen >> > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD REPLYlink written 12.2 years ago by James W. MacDonald52k
Hi Colleen, Colleen Doherty wrote: > Hi Benilton, > > Thanks! Updating affyio fixed the original reason I was trying to > make a new PDpackage in the first place. > > Previously, when using read.celfiles in oligo I was getting this error: > Error in .nextMethod(e1, e2) > updating affyio fixed that and I can now use read.celfiles with the > old pd.ath1.121510 > > I guess I don't need a new PDpackage now, but I still have a problem > making one- if the mistake is obvious to anyone I would appreciate > some advice. > > >> cdf<-"ATH1-121501.CDF" >> csv<-"ATH1-121501.na23.annot.csv" >> probe<-"ATH1-121501_probe_tab" >> makePDpackage(cdf,file1=csv, file2=probe, manufacturer="affymetrix", type="expression") > affymetrix expression > The package will be called pd.ath1.121501 > Reading CDF File > Reading Sequence Info > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > line 1 did not have 6 elements This is a pretty simple problem - scan() thinks there should be 6 things in the first line of the sequence file, and there are not. You can look at the top of the file using the 'head' function at a terminal prompt (e.g., head <thesequencefilenamehere>), which will print out the first 10 lines of the file. What you do about that is another question. It may be that this sequence file is different from the other Affy sequence files, and will require a fix in makePlatformDesign to accommodate, or you may have a corrupted file. Best, Jim > >> sessionInfo() > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] makePlatformDesign_1.2.0 affyio_1.6.0 oligo_1.2.0 > [4] oligoClasses_1.0.0 affxparser_1.10.0 AnnotationDbi_1.0.0 > [7] preprocessCore_1.0.0 RSQLite_0.6-3 DBI_0.2-3 > [10] Biobase_1.16.0 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-15 > > Thanks, > Colleen > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD REPLYlink written 12.2 years ago by James W. MacDonald52k
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