[aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed
Hi Henrik, Hi Pierre, Thanks a lot for your precious helps. Henrik , you are right: two files were not ofthe correct size: GenomeWIDEufl and GenomeWIDEugp. I downloaded them again from aroma.org Now, i will do the complete run of ACNE test of the GSE14996 dataset. Other questions will come... Here is my R session info R version 2.14.0 (2011-10-31) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ACNE_0.5.0 MASS_7.3-17aroma.affymetrix_2.5.0 [4] affxparser_1.26.4 aroma.apd_0.2.0R.huge_0.3.0 [7] aroma.core_2.5.0 aroma.light_1.22.0 R.rsp_0.7.5 [10] R.cache_0.6.1 R.filesets_1.1.5 digest_0.5.2 [13] R.utils_1.12.1 matrixStats_0.4.4 R.oo_1.9.3 [16] R.methodsS3_1.2.2 -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
[aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed
Hello, I follow the setup of the vignette but failed again setwd(c:/Users/foucault/Bioinformatic/acne/Test/) library(aroma.affymetrix); library(ACNE); verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - GSE14996,testSet; chipType - GenomeWideSNP_6; cdf - AffymetrixCdfFile$byChipType(chipType, tags=Full); print(cdf); AffymetrixCdfFile: Path: annotationData/chipTypes/GenomeWideSNP_6 Filename: GenomeWideSNP_6,Full.cdf Filesize: 470.44MB Chip type: GenomeWideSNP_6,Full RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 1881415 Cells per unit: 3.66 Number of QC units: 4 gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-05 10:12:33] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help, Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome
Re: [aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed
Hi, On Thu, Apr 5, 2012 at 10:17 AM, Frederic Foucault frederic.fouca...@gmail.com wrote: Hello, I follow the setup of the vignette but failed again setwd(c:/Users/foucault/Bioinformatic/acne/Test/) library(aroma.affymetrix); library(ACNE); verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - GSE14996,testSet; chipType - GenomeWideSNP_6; cdf - AffymetrixCdfFile$byChipType(chipType, tags=Full); print(cdf); AffymetrixCdfFile: Path: annotationData/chipTypes/GenomeWideSNP_6 Filename: GenomeWideSNP_6,Full.cdf Filesize: 470.44MB Chip type: GenomeWideSNP_6,Full RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 1881415 Cells per unit: 3.66 Number of QC units: 4 gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-05 10:12:33] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help, Frederic Did you place all the annotation files in the annotationData/chipTypes/GenomeWideSNP_6 folder ? It looks that this one is missing : GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp Do these file appear in the output of path - getPath(cdf) list.files(path) If not, then add them and retry. If yes then I'm missing something. Cheers, Pierre Pierre Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0
[aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed
Hi, Here is the path path - getPath(cdf) list.files(path) [1] GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl [3] GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
Re: [aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed
Hi, first of all, there is a very simple reason for this, we just have to find out why. My best guess now is that one of the files are incomplete. Start a fresh R session and verify that you get the exactly same *file sizes* as below: library(aroma.affymetrix); cdf - AffymetrixCdfFile$byChipType(GenomeWideSNP_6, tags=Full); ds - GenericDataFileSet$byPath(getPath(cdf)); print(as.list(ds)); [[1]] GenericDataFile: Name: GenomeWideSNP_6 Tags: Full,na31,hg19,HB20110328 Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl File size: 7.18 MB (7526452 bytes) RAM: 0.00 MB [[2]] GenericDataFile: Name: GenomeWideSNP_6 Tags: Full,na31,hg19,HB20110328 Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp File size: 8.97 MB (9407867 bytes) RAM: 0.00 MB [[3]] GenericDataFile: Name: GenomeWideSNP_6 Tags: Full Full name: GenomeWideSNP_6,Full Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.CDF File size: 470.44 MB (493291745 bytes) RAM: 0.00 MB [[4]] GenericDataFile: Name: GenomeWideSNP_6 Tags: HB20080710 Full name: GenomeWideSNP_6,HB20080710 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs File size: 170.92 MB (179217531 bytes) RAM: 0.00 MB /Henrik On Thu, Apr 5, 2012 at 5:40 AM, Frederic Foucault frederic.fouca...@gmail.com wrote: Hi, Here is the path path - getPath(cdf) list.files(path) [1] GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl [3] GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
Re: [aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed
...and by the way, what is your sessionInfo(), i.e. what does the following report? library(aroma.affymetrix); sessionInfo(); /Henrik On Thu, Apr 5, 2012 at 1:55 PM, Henrik Bengtsson henrik.bengts...@aroma-project.org wrote: Hi, first of all, there is a very simple reason for this, we just have to find out why. My best guess now is that one of the files are incomplete. Start a fresh R session and verify that you get the exactly same *file sizes* as below: library(aroma.affymetrix); cdf - AffymetrixCdfFile$byChipType(GenomeWideSNP_6, tags=Full); ds - GenericDataFileSet$byPath(getPath(cdf)); print(as.list(ds)); [[1]] GenericDataFile: Name: GenomeWideSNP_6 Tags: Full,na31,hg19,HB20110328 Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl File size: 7.18 MB (7526452 bytes) RAM: 0.00 MB [[2]] GenericDataFile: Name: GenomeWideSNP_6 Tags: Full,na31,hg19,HB20110328 Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp File size: 8.97 MB (9407867 bytes) RAM: 0.00 MB [[3]] GenericDataFile: Name: GenomeWideSNP_6 Tags: Full Full name: GenomeWideSNP_6,Full Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.CDF File size: 470.44 MB (493291745 bytes) RAM: 0.00 MB [[4]] GenericDataFile: Name: GenomeWideSNP_6 Tags: HB20080710 Full name: GenomeWideSNP_6,HB20080710 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs File size: 170.92 MB (179217531 bytes) RAM: 0.00 MB /Henrik On Thu, Apr 5, 2012 at 5:40 AM, Frederic Foucault frederic.fouca...@gmail.com wrote: Hi, Here is the path path - getPath(cdf) list.files(path) [1] GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl [3] GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf Frederic Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : Hello, I want to get allele specific copy number from SNP6 CL files I´m following the vignette for ACNE. I installed the annotation data in \test\annotationData\chipTypes \GenomeWideSNP6.0 GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are from aroma here is the error : gi - getGenomeInformation(cdf); Error in getGenomeInformation.AffymetrixCdfFile(cdf) : [2012-04-04 16:48:48] Exception: Failed to retrieve genome information for this chip type: GenomeWideSNP_6 at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Thank you for your help Frederic -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
