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. >> >> >>-- >>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(), 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/
