Re: [aroma.affymetrix] Problem with read CDF files
Hi Wero, Dario is right, as explained in http://aroma-project.org/node/66. Also, I would recommend not to manually add data in the installation directories of R packages. When you upgrade to a new version of R, your data will still be stuck in the installation directory of the old version. Specificially, I would avoid (1) having your 'annotationData' (and all the others aroma.* folders) in the directory where aroma.affymetrix is installed, and (2) using this installation directory as you working directory. See http://aroma-project.org/node/79 for an example of setup. Also, remember that 'annotationData' in the working directory can be a symbolic link to another directory on your file system. Hope this helps, Pierre On Mon, Sep 27, 2010 at 5:05 PM, Dario Strbenac d.strbe...@garvan.org.au wrote: Hello, You need to be in the directory above annotationData. - Dario. Original message Date: Mon, 27 Sep 2010 16:53:06 -0700 (PDT) From: aroma-affymetrix@googlegroups.com (on behalf of Wero ivansk...@gmail.com) Subject: [aroma.affymetrix] Problem with read CDF files To: aroma.affymetrix aroma-affymetrix@googlegroups.com Cc: ii...@inmegen.gob.mx Hi, I have been trying to read the CDF files for the HuGene-1_0-st-v1 array with aroma.affymetrix and it has been very confuse for me. I have the correct CDF files from the aroma page. The CDF files are in the path: /Library/Frameworks/R.framework/ Versions/2.11/Resources/library/aroma.affymetrix/annotationData/ chipTypes/HuGene-1_0-st-v1. My working directory is: annotationData but I still have this error: # cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3) Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = r3)` = environment, : [2010-09-27 06:14:53] Exception: Could not locate a file for this chip type: HuGene-1_0-st-v1,r3 at throw(Exception(...)) at throw.default(Could not locate a file for this chip type: , pa at throw(Could not locate a file for this chip type: , paste(c(ch at method(static, ...) at AffymetrixCdfFile$byChipType(chipType, tags = r3) ## Also, if I look for the cdf path file in R, it returns NULL pathname - annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf cdf - AffymetrixCdfFile(pathname) Error in list(`AffymetrixCdfFile(pathname)` = environment, `extend(AromaChipTypeAnnotationFile(...), c(AffymetrixCdfFile, ` = environment, : [2010-09-27 06:48:54] Exception: Pathname not found: annotationData/ chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf (none of the parent directories [annotationData/chipTypes/HuGene-1_0-st-v1/] exist; current directory is '/Library/Frameworks/R.framework/Versions/2.11/ Resources/library/aroma.affymetrix/annotationData/chipTypes/HuGene-1_0- st-v1') at throw(Exception(...)) at throw.default(Pathname not found: , pathname, reason) at throw(Pathname not found: , pathname, reason) at method(static, ...) at Arguments$getReadablePathname(filename, path = path, mustExist = at GenericDataFile(...) at extend(GenericDataFile(...), AromaMicroarrayDataFile) at AromaMicroarrayDataFile(...) at extend(AromaMicroarrayDataFile(...), c(AffymetrixFile, uses(A at AffymetrixFile(...) at extend(AffymetrixFile(...), AromaChipTypeAnnotationFile) at AromaChipTypeAnnotationFile(...) at extend(AromaChipTypeAnnotationFile(...), c(AffymetrixCdfFile, at Affymetrix In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' pathname - getPathname(cdf) print(pathname) [1] annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st- v1,r3.cdf pathname2 - AffymetrixCdfFile$findByChipType(HuGene-1_0-st-v1, tags=3) print(pathname2) NULL ### This is my sessionInfo() R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] oligoClasses_1.10.0 Biobase_2.8.0 [3] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 [5] affxparser_1.20.0 R.huge_0.2.0 [7] aroma.core_1.7.0 aroma.light_1.16.1 [9] matrixStats_0.2.1 R.rsp_0.4.0 [11] R.cache_0.3.0 R.filesets_0.9.0 [13] digest_0.4.2 R.utils_1.5.2 [15] R.oo_1.7.4 oligo_1.12.2 [17] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affyio_1.16.0 Biostrings_2.16.5 DBI_0.2-5 [4] IRanges_1.6.6 preprocessCore_1.10.0 splines_2.11.1 [7] tools_2.11.1 This is my traceback() 6: throw.Exception(Exception(...)) 5: throw(Exception(...)) 4: throw.default(msg) 3: throw(msg) 2: method(static, ...) 1: AffymetrixCdfFile$fromChipType(HuGene-1_0-st-v1, tags = r3) ### I would appreciate any help, thanks!!! Wero
Re: [aroma.affymetrix] Problem with read CDF files
Hello, You need to be in the directory above annotationData. - Dario. Original message Date: Mon, 27 Sep 2010 16:53:06 -0700 (PDT) From: aroma-affymetrix@googlegroups.com (on behalf of Wero ivansk...@gmail.com) Subject: [aroma.affymetrix] Problem with read CDF files To: aroma.affymetrix aroma-affymetrix@googlegroups.com Cc: ii...@inmegen.gob.mx Hi, I have been trying to read the CDF files for the HuGene-1_0-st-v1 array with aroma.affymetrix and it has been very confuse for me. I have the correct CDF files from the aroma page. The CDF files are in the path: /Library/Frameworks/R.framework/ Versions/2.11/Resources/library/aroma.affymetrix/annotationData/ chipTypes/HuGene-1_0-st-v1. My working directory is: annotationData but I still have this error: # cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3) Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = r3)` = environment, : [2010-09-27 06:14:53] Exception: Could not locate a file for this chip type: HuGene-1_0-st-v1,r3 at throw(Exception(...)) at throw.default(Could not locate a file for this chip type: , pa at throw(Could not locate a file for this chip type: , paste(c(ch at method(static, ...) at AffymetrixCdfFile$byChipType(chipType, tags = r3) ## Also, if I look for the cdf path file in R, it returns NULL pathname - annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf cdf - AffymetrixCdfFile(pathname) Error in list(`AffymetrixCdfFile(pathname)` = environment, `extend(AromaChipTypeAnnotationFile(...), c(AffymetrixCdfFile, ` = environment, : [2010-09-27 06:48:54] Exception: Pathname not found: annotationData/ chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf (none of the parent directories [annotationData/chipTypes/HuGene-1_0-st-v1/] exist; current directory is '/Library/Frameworks/R.framework/Versions/2.11/ Resources/library/aroma.affymetrix/annotationData/chipTypes/HuGene-1_0- st-v1') at throw(Exception(...)) at throw.default(Pathname not found: , pathname, reason) at throw(Pathname not found: , pathname, reason) at method(static, ...) at Arguments$getReadablePathname(filename, path = path, mustExist = at GenericDataFile(...) at extend(GenericDataFile(...), AromaMicroarrayDataFile) at AromaMicroarrayDataFile(...) at extend(AromaMicroarrayDataFile(...), c(AffymetrixFile, uses(A at AffymetrixFile(...) at extend(AffymetrixFile(...), AromaChipTypeAnnotationFile) at AromaChipTypeAnnotationFile(...) at extend(AromaChipTypeAnnotationFile(...), c(AffymetrixCdfFile, at Affymetrix In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' pathname - getPathname(cdf) print(pathname) [1] annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st- v1,r3.cdf pathname2 - AffymetrixCdfFile$findByChipType(HuGene-1_0-st-v1, tags=3) print(pathname2) NULL ### This is my sessionInfo() R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] oligoClasses_1.10.0Biobase_2.8.0 [3] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 [5] affxparser_1.20.0 R.huge_0.2.0 [7] aroma.core_1.7.0 aroma.light_1.16.1 [9] matrixStats_0.2.1 R.rsp_0.4.0 [11] R.cache_0.3.0 R.filesets_0.9.0 [13] digest_0.4.2 R.utils_1.5.2 [15] R.oo_1.7.4 oligo_1.12.2 [17] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affyio_1.16.0 Biostrings_2.16.5 DBI_0.2-5 [4] IRanges_1.6.6 preprocessCore_1.10.0 splines_2.11.1 [7] tools_2.11.1 This is my traceback() 6: throw.Exception(Exception(...)) 5: throw(Exception(...)) 4: throw.default(msg) 3: throw(msg) 2: method(static, ...) 1: AffymetrixCdfFile$fromChipType(HuGene-1_0-st-v1, tags = r3) ### I would appreciate any help, thanks!!! Wero. -- 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/ -- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia -- 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
