Question: oligo package
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Hi all, I've been working on R/Bioconductor for the last month and i'm still quite confused on many ways. Im currently trying to process an expression microarray dataset with Affymetrix chip (hugene.1.1.st.v1). Questions are actually multiple. I get an error when im trying to load the phenodata with the read.celfiles command saying sample names are different between phenodata and protocol data and phenodata and featuredata: Error in validObject(out) : invalid class ???GeneFeatureSet??? object: 1: sampleNames differ between assayData and phenoData invalid class ???GeneFeatureSet??? object: 2: sampleNames differ between phenoData and protocolData Also i have no clues how to annotate my expression data as i cant even find commands to access the annotation package. Sorry for the non-precise questions. I tried to read as much as i could and asked everyone in the dep but im still stuck here. Thank you very much Bruno -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2 [3] DBI_0.2-5 oligo_1.22.0 [5] Biobase_2.18.0 oligoClasses_1.20.0 [7] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affyio_1.26.0 BiocInstaller_1.8.3 [4] Biostrings_2.26.2 bit_1.1-9 codetools_0.2-8 [7] ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 [10] IRanges_1.16.4 iterators_1.0.6 parallel_2.15.1 [13] preprocessCore_1.20.0 splines_2.15.1 stats4_2.15.1 [16] tools_2.15.1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 7.0 years ago by James W. MacDonald52k • written 7.0 years ago by Guest User12k
Answer: oligo package
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ok sorry ill copy and past all the steps i've done after loading the "oligo" package. Thanks a lot celfiles<-list.celfiles() > celfiles [1] "Titan_0026_838M_Freeman_838M_A1_A05.CEL" "Titan_0026_838M_Freeman_838M_A1_E09.CEL" "Titan_0026_838M_Freeman_838M_A10_B07.CEL" [4] "Titan_0026_838M_Freeman_838M_A2_B05.CEL" "Titan_0026_838M_Freeman_838M_A3_C05.CEL" "Titan_0026_838M_Freeman_838M_A3_F09.CEL" [7] "Titan_0026_838M_Freeman_838M_A4_D05.CEL" "Titan_0026_838M_Freeman_838M_A5_E05.CEL" "Titan_0026_838M_Freeman_838M_A6_F05.CEL" [10] "Titan_0026_838M_Freeman_838M_A7_G05.CEL" "Titan_0026_838M_Freeman_838M_A8_H05.CEL" "Titan_0026_838M_Freeman_838M_A9_A07.CEL" [13] "Titan_0026_838M_Freeman_838M_B1_C07.CEL" "Titan_0026_838M_Freeman_838M_B1_G09.CEL" "Titan_0026_838M_Freeman_838M_B10_D09.CEL" [16] "Titan_0026_838M_Freeman_838M_B2_D07.CEL" "Titan_0026_838M_Freeman_838M_B3_E07.CEL" "Titan_0026_838M_Freeman_838M_B4_F07.CEL" [19] "Titan_0026_838M_Freeman_838M_B4_H09.CEL" "Titan_0026_838M_Freeman_838M_B5_G07.CEL" "Titan_0026_838M_Freeman_838M_B6_H07.CEL" [22] "Titan_0026_838M_Freeman_838M_B7_A09.CEL" "Titan_0026_838M_Freeman_838M_B8_B09.CEL" "Titan_0026_838M_Freeman_838M_B9_C09.CEL" > pd<-read.table("phenodata.txt") > pd<-as(pd, "AnnotatedDataFrame") >TFdata<-read.celfiles(celfiles, phenoData=pd) Platform design info loaded. Reading in : Titan_0026_838M_Freeman_838M_A1_A05.CEL Reading in : Titan_0026_838M_Freeman_838M_A1_E09.CEL Reading in : Titan_0026_838M_Freeman_838M_A10_B07.CEL Reading in : Titan_0026_838M_Freeman_838M_A2_B05.CEL Reading in : Titan_0026_838M_Freeman_838M_A3_C05.CEL Reading in : Titan_0026_838M_Freeman_838M_A3_F09.CEL Reading in : Titan_0026_838M_Freeman_838M_A4_D05.CEL Reading in : Titan_0026_838M_Freeman_838M_A5_E05.CEL Reading in : Titan_0026_838M_Freeman_838M_A6_F05.CEL Reading in : Titan_0026_838M_Freeman_838M_A7_G05.CEL Reading in : Titan_0026_838M_Freeman_838M_A8_H05.CEL Reading in : Titan_0026_838M_Freeman_838M_A9_A07.CEL Reading in : Titan_0026_838M_Freeman_838M_B1_C07.CEL Reading in : Titan_0026_838M_Freeman_838M_B1_G09.CEL Reading in : Titan_0026_838M_Freeman_838M_B10_D09.CEL Reading in : Titan_0026_838M_Freeman_838M_B2_D07.CEL Reading in : Titan_0026_838M_Freeman_838M_B3_E07.CEL Reading in : Titan_0026_838M_Freeman_838M_B4_F07.CEL Reading in : Titan_0026_838M_Freeman_838M_B4_H09.CEL Reading in : Titan_0026_838M_Freeman_838M_B5_G07.CEL Reading in : Titan_0026_838M_Freeman_838M_B6_H07.CEL Reading in : Titan_0026_838M_Freeman_838M_B7_A09.CEL Reading in : Titan_0026_838M_Freeman_838M_B8_B09.CEL Reading in : Titan_0026_838M_Freeman_838M_B9_C09.CEL Error in validObject(out) : invalid class ???GeneFeatureSet??? object: 1: sampleNames differ between assayData and phenoData invalid class ???GeneFeatureSet??? object: 2: sampleNames differ between phenoData and protocolData -- output of sessionInfo(): sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 [7] BiocGenerics_0.4.0 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affyio_1.26.0 Biostrings_2.26.2 bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 [8] GenomicRanges_1.10.5 IRanges_1.16.4 iterators_1.0.6 parallel_2.15.1 preprocessCore_1.20.0 splines_2.15.1 stats4_2.15.1 [15] tools_2.15.1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink written 7.0 years ago by Guest User12k
Answer: oligo package
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7.0 years ago by
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James W. MacDonald52k wrote:
Hi Bruno, On 12/6/2012 12:05 PM, Bruno [guest] wrote: > Hi all, > I've been working on R/Bioconductor for the last month and i'm still quite confused on many ways. Im currently trying to process an expression microarray dataset with Affymetrix chip (hugene.1.1.st.v1). Questions are actually multiple. I get an error when im trying to load the phenodata with the read.celfiles command saying sample names are different between phenodata and protocol data and phenodata and featuredata: > Error in validObject(out) : > invalid class ???GeneFeatureSet??? object: 1: sampleNames differ between assayData and phenoData > invalid class ???GeneFeatureSet??? object: 2: sampleNames differ between phenoData and protocolData > Also i have no clues how to annotate my expression data as i cant even find commands to access the annotation package. Sorry for the non-precise questions. I tried to read as much as i could and asked everyone in the dep but im still stuck here. Thank you very much There isn't really a problem with your questions, but you don't give us enough to go on. When asking questions, you have to always think about what information will be useful to those who might answer. I can pretty much condense what you have told us into 'I did some stuff and here are the errors'. But what you aren't telling us is EXACTLY what did you do? And the only way to really tell us is to copy and paste the R commands you are using, right up to the point you get the error. So show us your code, and perhaps we can help. Best, Jim > Bruno > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2 > [3] DBI_0.2-5 oligo_1.22.0 > [5] Biobase_2.18.0 oligoClasses_1.20.0 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.30.0 affyio_1.26.0 BiocInstaller_1.8.3 > [4] Biostrings_2.26.2 bit_1.1-9 codetools_0.2-8 > [7] ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 > [10] IRanges_1.16.4 iterators_1.0.6 parallel_2.15.1 > [13] preprocessCore_1.20.0 splines_2.15.1 stats4_2.15.1 > [16] tools_2.15.1 zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 7.0 years ago by James W. MacDonald52k
Answer: oligo package
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7.0 years ago by
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James W. MacDonald52k wrote:
On 12/6/2012 1:59 PM, Bruno [guest] wrote: > ok sorry ill copy and past all the steps i've done after loading the "oligo" package. > Thanks a lot > > celfiles<-list.celfiles() >> celfiles > [1] "Titan_0026_838M_Freeman_838M_A1_A05.CEL" "Titan_0026_838M_Freeman_838M_A1_E09.CEL" "Titan_0026_838M_Freeman_838M_A10_B07.CEL" > [4] "Titan_0026_838M_Freeman_838M_A2_B05.CEL" "Titan_0026_838M_Freeman_838M_A3_C05.CEL" "Titan_0026_838M_Freeman_838M_A3_F09.CEL" > [7] "Titan_0026_838M_Freeman_838M_A4_D05.CEL" "Titan_0026_838M_Freeman_838M_A5_E05.CEL" "Titan_0026_838M_Freeman_838M_A6_F05.CEL" > [10] "Titan_0026_838M_Freeman_838M_A7_G05.CEL" "Titan_0026_838M_Freeman_838M_A8_H05.CEL" "Titan_0026_838M_Freeman_838M_A9_A07.CEL" > [13] "Titan_0026_838M_Freeman_838M_B1_C07.CEL" "Titan_0026_838M_Freeman_838M_B1_G09.CEL" "Titan_0026_838M_Freeman_838M_B10_D09.CEL" > [16] "Titan_0026_838M_Freeman_838M_B2_D07.CEL" "Titan_0026_838M_Freeman_838M_B3_E07.CEL" "Titan_0026_838M_Freeman_838M_B4_F07.CEL" > [19] "Titan_0026_838M_Freeman_838M_B4_H09.CEL" "Titan_0026_838M_Freeman_838M_B5_G07.CEL" "Titan_0026_838M_Freeman_838M_B6_H07.CEL" > [22] "Titan_0026_838M_Freeman_838M_B7_A09.CEL" "Titan_0026_838M_Freeman_838M_B8_B09.CEL" "Titan_0026_838M_Freeman_838M_B9_C09.CEL" >> pd<-read.table("phenodata.txt") >> pd<-as(pd, "AnnotatedDataFrame") >> TFdata<-read.celfiles(celfiles, phenoData=pd) > Platform design info loaded. > Reading in : Titan_0026_838M_Freeman_838M_A1_A05.CEL > Reading in : Titan_0026_838M_Freeman_838M_A1_E09.CEL > Reading in : Titan_0026_838M_Freeman_838M_A10_B07.CEL > Reading in : Titan_0026_838M_Freeman_838M_A2_B05.CEL > Reading in : Titan_0026_838M_Freeman_838M_A3_C05.CEL > Reading in : Titan_0026_838M_Freeman_838M_A3_F09.CEL > Reading in : Titan_0026_838M_Freeman_838M_A4_D05.CEL > Reading in : Titan_0026_838M_Freeman_838M_A5_E05.CEL > Reading in : Titan_0026_838M_Freeman_838M_A6_F05.CEL > Reading in : Titan_0026_838M_Freeman_838M_A7_G05.CEL > Reading in : Titan_0026_838M_Freeman_838M_A8_H05.CEL > Reading in : Titan_0026_838M_Freeman_838M_A9_A07.CEL > Reading in : Titan_0026_838M_Freeman_838M_B1_C07.CEL > Reading in : Titan_0026_838M_Freeman_838M_B1_G09.CEL > Reading in : Titan_0026_838M_Freeman_838M_B10_D09.CEL > Reading in : Titan_0026_838M_Freeman_838M_B2_D07.CEL > Reading in : Titan_0026_838M_Freeman_838M_B3_E07.CEL > Reading in : Titan_0026_838M_Freeman_838M_B4_F07.CEL > Reading in : Titan_0026_838M_Freeman_838M_B4_H09.CEL > Reading in : Titan_0026_838M_Freeman_838M_B5_G07.CEL > Reading in : Titan_0026_838M_Freeman_838M_B6_H07.CEL > Reading in : Titan_0026_838M_Freeman_838M_B7_A09.CEL > Reading in : Titan_0026_838M_Freeman_838M_B8_B09.CEL > Reading in : Titan_0026_838M_Freeman_838M_B9_C09.CEL > Error in validObject(out) : > invalid class ???GeneFeatureSet??? object: 1: sampleNames differ between assayData and phenoData > invalid class ???GeneFeatureSet??? object: 2: sampleNames differ between phenoData and protocolData OK, this is a bit better, although it is still a mystery what is in your phenoData. However, the error messages say what the problem is - the phenoData object that you are trying to put in your GeneFeatureSet is incompatible. Now I am no expert on the intricacies of the phenoData slot, because I actually never use it. So unless you are planning on doing things with the phenoData slot, you can just go forward without specifying it directly: TFdata<-read.celfiles(celfiles) ## side note - spaces are good However, it isn't difficult to see what is expected. We can just open up an existing ExpressionSet (which GeneFeatureSet is a subset of), and see what is in there: > library(affydata) > data(Dilution) > pData(phenoData(Dilution)) liver sn19 scanner 20A 20 0 1 20B 20 0 2 10A 10 0 1 10B 10 0 2 > sampleNames(Dilution) [1] "20A" "20B" "10A" "10B" So there are four samples here, and the row names of the phenoData match those sample names. So the first step for you is to ensure that the row names of the data.frame you are using to create the phenoData are identical to the sampleNames that will result (e.g., they should be identical to your celfiles variable). Best, Jim > > -- output of sessionInfo(): > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 > [7] BiocGenerics_0.4.0 BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] affxparser_1.30.0 affyio_1.26.0 Biostrings_2.26.2 bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 > [8] GenomicRanges_1.10.5 IRanges_1.16.4 iterators_1.0.6 parallel_2.15.1 preprocessCore_1.20.0 splines_2.15.1 stats4_2.15.1 > [15] tools_2.15.1 zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 7.0 years ago by James W. MacDonald52k
If you can guarantee that the order of samples in your txt file is the same as in your 'celfiles' variables, you should be okay with: pd <- read.table("phenodata.txt"**) pd <- as(pd, "AnnotatedDataFrame") TFdata <- read.celfiles(**celfiles) sampleNames(pd) <- sampleNames(TFdata) phenoData(pd) <- pd b On 6 December 2012 19:13, James W. MacDonald <jmacdon@uw.edu> wrote: > > > On 12/6/2012 1:59 PM, Bruno [guest] wrote: > >> ok sorry ill copy and past all the steps i've done after loading the >> "oligo" package. >> Thanks a lot >> >> celfiles<-list.celfiles() >> >>> celfiles >>> >> [1] "Titan_0026_838M_Freeman_838M_**A1_A05.CEL" >> "Titan_0026_838M_Freeman_838M_**A1_E09.CEL" >> "Titan_0026_838M_Freeman_838M_**A10_B07.CEL" >> [4] "Titan_0026_838M_Freeman_838M_**A2_B05.CEL" >> "Titan_0026_838M_Freeman_838M_**A3_C05.CEL" >> "Titan_0026_838M_Freeman_838M_**A3_F09.CEL" >> [7] "Titan_0026_838M_Freeman_838M_**A4_D05.CEL" >> "Titan_0026_838M_Freeman_838M_**A5_E05.CEL" >> "Titan_0026_838M_Freeman_838M_**A6_F05.CEL" >> [10] "Titan_0026_838M_Freeman_838M_**A7_G05.CEL" >> "Titan_0026_838M_Freeman_838M_**A8_H05.CEL" >> "Titan_0026_838M_Freeman_838M_**A9_A07.CEL" >> [13] "Titan_0026_838M_Freeman_838M_**B1_C07.CEL" >> "Titan_0026_838M_Freeman_838M_**B1_G09.CEL" >> "Titan_0026_838M_Freeman_838M_**B10_D09.CEL" >> [16] "Titan_0026_838M_Freeman_838M_**B2_D07.CEL" >> "Titan_0026_838M_Freeman_838M_**B3_E07.CEL" >> "Titan_0026_838M_Freeman_838M_**B4_F07.CEL" >> [19] "Titan_0026_838M_Freeman_838M_**B4_H09.CEL" >> "Titan_0026_838M_Freeman_838M_**B5_G07.CEL" >> "Titan_0026_838M_Freeman_838M_**B6_H07.CEL" >> [22] "Titan_0026_838M_Freeman_838M_**B7_A09.CEL" >> "Titan_0026_838M_Freeman_838M_**B8_B09.CEL" >> "Titan_0026_838M_Freeman_838M_**B9_C09.CEL" >> >>> pd<-read.table("phenodata.txt"**) >>> pd<-as(pd, "AnnotatedDataFrame") >>> TFdata<-read.celfiles(**celfiles, phenoData=pd) >>> >> Platform design info loaded. >> Reading in : Titan_0026_838M_Freeman_838M_**A1_A05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A1_E09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A10_B07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A2_B05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A3_C05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A3_F09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A4_D05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A5_E05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A6_F05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A7_G05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A8_H05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A9_A07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B1_C07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B1_G09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B10_D09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B2_D07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B3_E07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B4_F07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B4_H09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B5_G07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B6_H07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B7_A09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B8_B09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B9_C09.CEL >> >> Error in validObject(out) : >> invalid class “GeneFeatureSet†object: 1: sampleNames differ >> between assayData and phenoData >> invalid class “GeneFeatureSet†object: 2: sampleNames differ between >> phenoData and protocolData >> > > OK, this is a bit better, although it is still a mystery what is in your > phenoData. However, the error messages say what the problem is - the > phenoData object that you are trying to put in your GeneFeatureSet is > incompatible. > > Now I am no expert on the intricacies of the phenoData slot, because I > actually never use it. So unless you are planning on doing things with the > phenoData slot, you can just go forward without specifying it directly: > > TFdata<-read.celfiles(**celfiles) ## side note - spaces are good > > > However, it isn't difficult to see what is expected. We can just open up > an existing ExpressionSet (which GeneFeatureSet is a subset of), and see > what is in there: > > > library(affydata) > > data(Dilution) > > pData(phenoData(Dilution)) > liver sn19 scanner > 20A 20 0 1 > 20B 20 0 2 > 10A 10 0 1 > 10B 10 0 2 > > sampleNames(Dilution) > [1] "20A" "20B" "10A" "10B" > > So there are four samples here, and the row names of the phenoData match > those sample names. So the first step for you is to ensure that the row > names of the data.frame you are using to create the phenoData are identical > to the sampleNames that will result (e.g., they should be identical to your > celfiles variable). > > Best, > > Jim > > > >> -- output of sessionInfo(): >> >> >> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C >> >> [5] LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] pd.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 >> oligo_1.22.0 Biobase_2.18.0 >> oligoClasses_1.20.0 >> [7] BiocGenerics_0.4.0 BiocInstaller_1.8.3 >> >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.30.0 affyio_1.26.0 Biostrings_2.26.2 >> bit_1.1-9 codetools_0.2-8 ff_2.2-10 >> foreach_1.4.0 >> [8] GenomicRanges_1.10.5 IRanges_1.16.4 iterators_1.0.6 >> parallel_2.15.1 preprocessCore_1.20.0 splines_2.15.1 >> stats4_2.15.1 >> [15] tools_2.15.1 zlibbioc_1.4.0 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 7.0 years ago by Benilton Carvalho4.3k
Hi List, I am having a problem reading HuGene 1.0 arrays with the oligo package. library(oligo) read.celfiles(filenames=filenames) # Could not open file ~/Downloads/SSA/original/CC_Black_(HuGene-1_0-st-v1).CEL Looking inside read.celfiles, it seems that the problem may start with getCelChipType oligo:::getCelChipType(filenames[1],TRUE) Error in read.celfile.header(x) : Could not open file ~/Downloads/SSA/original/CC_Black_(HuGene-1_0-st-v1).CEL changing the useAffyio to FALSE seems to work. oligo:::getCelChipType(filenames[1],useAffyio=FALSE) [1] "HuGene-1_0-st-v1" However the useAffyio option has been removed from read.celfiles and changing read.celfiles at this point just moves the problem further down into the function. Bye Rob > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hugene.1.0.st.v1_3.6.0 RSQLite_0.11.2 [3] DBI_0.2-5 oligo_1.20.4 [5] oligoClasses_1.18.0 loaded via a namespace (and not attached): [1] affxparser_1.28.1 affyio_1.24.0 Biobase_2.16.0 [4] BiocGenerics_0.2.0 BiocInstaller_1.4.9 Biostrings_2.24.1 [7] bit_1.1-9 codetools_0.2-8 ff_2.2-10 [10] foreach_1.4.0 IRanges_1.14.4 iterators_1.0.6 [13] preprocessCore_1.18.0 splines_2.15.2 stats4_2.15.2 [16] tools_2.15.2 zlibbioc_1.2.0 -- Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 CSIRO Mathematical and Information Sciences +61 2 9325 3100 Locked Bag 17, North Ryde, New South Wales, Australia, 1670 http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au Java has certainly revolutionized marketing and litigation.
ADD REPLYlink written 7.0 years ago by Rob Dunne230
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