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/.
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--------------------------------------
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/
