[aroma.affymetrix] Problem with read CDF files

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[aroma.affymetrix] Problem with read CDF files

Wero
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.


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Re: [aroma.affymetrix] Problem with read CDF files

Dario Strbenac
Hello,

You need to be in the directory above annotationData.

- Dario.

---- Original message ----

>Date: Mon, 27 Sep 2010 16:53:06 -0700 (PDT)
>From: [hidden email] (on behalf of Wero <[hidden email]>)
>Subject: [aroma.affymetrix] Problem with read CDF files  
>To: "aroma.affymetrix" <[hidden email]>
>Cc: [hidden email]
>
>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 [hidden email]
>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 [hidden email]
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Re: [aroma.affymetrix] Problem with read CDF files

Pierre Neuvial
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
<[hidden email]> 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: [hidden email] (on behalf of Wero <[hidden email]>)
>>Subject: [aroma.affymetrix] Problem with read CDF files
>>To: "aroma.affymetrix" <[hidden email]>
>>Cc: [hidden email]
>>
>>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 [hidden email]
>>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 [hidden email]
> 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 [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/