Dear Narwin,
please see the message that I've sent you offline and continue any
correspondence there instead of here.
/Henrik
On Wed, May 1, 2013 at 8:17 AM, nawin MOHAMMED <nawi...@gmail.com> wrote:
> hi henrik ,
>
> please i can understand what is the problem ??? iam using R3 with 64X and
> i try what you tolde me also i call for list file as bellow
>
>> pathAC <- Arguments$getReadablePath("annotationData/HG-U133_Plus_2",
>> mustExist=TRUE)
> [2013-05-01 15:32:56] Exception: Pathname not found:
> annotationData/HG-U133_Plus_2 (none of the parent directories
> [annotationData/] exist; current directory is
> 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2')
>
> at #05. getReadablePathname.Arguments(static, path = path, mustExist =
> mustExist,
> ...)
> - getReadablePathname.Arguments() is in environment 'R.utils'
>
> at #04. getReadablePathname(static, path = path, mustExist = mustExist,
> ...)
> - getReadablePathname() is in environment 'R.utils'
>
> at #03. getReadablePath.Arguments(static, ...)
> - getReadablePath.Arguments() is in environment 'R.utils'
>
> at #02. getReadablePath(static, ...)
> - getReadablePath() is in environment 'R.utils'
> - originating from '<text>'
>
> at #01. Arguments$getReadablePath("annotationData/HG-U133_Plus_2",
> mustExist = TRUE)
> - Arguments$getReadablePath() is local of the calling function
>
> Error: Pathname not found: annotationData/HG-U133_Plus_2 (none of the parent
> directories [annotationData/] exist; current directory is
> 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2')
> In addition: Warning messages:
> 1: In is.na(parent) :
> is.na() applied to non-(list or vector) of type 'NULL'
> 2: In is.na(parent) :
> is.na() applied to non-(list or vector) of type 'NULL'
>> library("R.utils")
>> pathAC <-
>> Arguments$getReadablePath("AromaAnalysis/annotationData/HG-U133_Plus_2",
>> mustExist=TRUE)
> [2013-05-01 16:06:11] Exception: Pathname not found:
> AromaAnalysis/annotationData/HG-U133_Plus_2 (none of the parent directories
> [AromaAnalysis/annotationData/] exist; current directory is
> 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2')
>
> at #05. getReadablePathname.Arguments(static, path = path, mustExist =
> mustExist,
> ...)
> - getReadablePathname.Arguments() is in environment 'R.utils'
>
> at #04. getReadablePathname(static, path = path, mustExist = mustExist,
> ...)
> - getReadablePathname() is in environment 'R.utils'
>
> at #03. getReadablePath.Arguments(static, ...)
> - getReadablePath.Arguments() is in environment 'R.utils'
>
> at #02. getReadablePath(static, ...)
> - getReadablePath() is in environment 'R.utils'
> - originating from '<text>'
>
> at #01.
> Arguments$getReadablePath("AromaAnalysis/annotationData/HG-U133_Plus_2",
> mustExist = TRUE)
> - Arguments$getReadablePath() is local of the calling function
>
> Error: Pathname not found: AromaAnalysis/annotationData/HG-U133_Plus_2 (none
> of the parent directories [AromaAnalysis/annotationData/] exist; current
> directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2')
> 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'
>> list.files()
> [1] "HG-U133_Plus_2.cdf"
>>
>
>
>
>
>
>
> On Tuesday, April 30, 2013 5:02:48 PM UTC+1, Henrik Bengtsson wrote:
>>
>> Hi.
>>
>> On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED <naw...@gmail.com> wrote:
>> > hi Pierre,
>> >
>> > the anootationData is allocated by default in the aroma.affymetrix ??
>> > is it
>> > ??? as its declare in the page of aroma :
>> >
>> > Aroma.affymetrix searches for CDF files in the annotationData/ directory
>> > of
>> > the current working directory. Place the CDF for chip type <chipType>
>> > in a
>> > directory of format:
>> >
>> > annotationData/chipTypes/<chip type>/
>> >
>> >
>> > and my location is
>> >
>> >
>> > "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2
>> >
>> > i just creat new folder in annotation data with name chip type and
>> > inside
>> > it another folder with chip name ???
>> > iam just confused ??
>>
>> What you're missing in "Aroma.affymetrix searches for CDF files in the
>> annotationData/ directory of the current working directory" is the
>> part that says ***of the current working directory***. In other
>> words, in your current working directory (i.e. getwd()) you should see
>> subdirectory "annotationData" if you call list.files(). You may find
>> the following page useful too:
>>
>> http://aroma-project.org/troubleshooting/DirectoryStructures
>>
>>
>>
>> Also, I strongly recommend to put your data files (annotationData/,
>> rawData/, etc.) somewhere else than where R installs packages. Right
>> now you seem to place them in:
>>
>>
>> C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2
>>
>> The directory 'C:/Users/nwayyin/Documents/R/win-library/3.0/' is where
>> R install packages and you shouldn't add/remove things from there.
>> For instance, if you uninstall aroma.affymetrix then all your data may
>> disappear as well. Instead, let your working directory be something
>> like:
>>
>> C:/Users/nwayyin/AromaAnalysis/
>>
>> and let that be your working directory in R.
>>
>> /Henrik
>>
>> > why this error occur please if you know the cause of problem
>> > please
>> > tell me
>> >
>> >
>> > On Tuesday, April 30, 2013 3:16:00 PM UTC+1, Pierre Neuvial wrote:
>> >>
>> >> Hi,
>> >>
>> >> Quoting myself,
>> >>
>> >> "1. Read carefully the setup page: http://www.aroma-project.org/setup,
>> >> and follow the links in that page."
>> >>
>> >> The first link "Location of annotation data files" explains where
>> >> annotation data files should be located.
>> >>
>> >> Best,
>> >>
>> >> Pierre
>> >>
>> >>
>> >> On Tue, Apr 30, 2013 at 2:10 PM, nawin MOHAMMED <naw...@gmail.com>
>> >> wrote:
>> >> >
>> >> > i also down load the CDF from affymetrix but its not working
>> >> > same
>> >> > problem
>> >> >
>> >> > Error: Failed to create AffymetrixCdfFile object. Could not locate an
>> >> > annotation data file for chip type 'HG-U133_Plus_2' with tags 'full'
>> >> > and
>> >> > with filename extension 'cdf'.
>> >> >> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2",tags="full")
>> >> > [2013-04-30 13:08:07] Exception: Failed to create AffymetrixCdfFile
>> >> > object.
>> >> > Could not locate an annotation data file for chip type
>> >> > 'HG-U133_Plus_2'
>> >> > with
>> >> > tags 'full' and with filename extension 'cdf'.
>> >> >
>> >> > at #03. byChipType.UnitAnnotationDataFile(static, ...)
>> >> > - byChipType.UnitAnnotationDataFile() is in environment
>> >> > 'aroma.core'
>> >> >
>> >> > at #02. byChipType(static, ...)
>> >> > - byChipType() is in environment 'aroma.core'
>> >> > - originating from '<text>'
>> >> >
>> >> > at #01. AffymetrixCdfFile$byChipType("HG-U133_Plus_2", tags =
>> >> > "full")
>> >> > - AffymetrixCdfFile$byChipType() is local of the calling
>> >> > function
>> >> >
>> >> > Error: Failed to create AffymetrixCdfFile object. Could not locate an
>> >> > annotation data file for chip type 'HG-U133_Plus_2' with tags 'full'
>> >> > and
>> >> > with filename extension 'cdf'.
>> >> >> getwd()
>> >> > [1]
>> >> >
>> >> >
>> >> > "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/CD_hgu133a2_libraryfile"
>> >> >>
>> >> >
>> >> >
>> >> > On Tuesday, April 30, 2013 8:40:35 AM UTC+1, Pierre Neuvial wrote:
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> Please create a new thread (with a relevant subject line) instead of
>> >> >> replying to an unrelated one.
>> >> >>
>> >> >> See below.
>> >> >>
>> >> >> On Tue, Apr 30, 2013 at 9:22 AM, nawin MOHAMMED <naw...@gmail.com>
>> >> >> wrote:
>> >> >> >
>> >> >> >
>> >> >> > Greeting ,
>> >> >> >
>> >> >> > iam a Phd student , i try implement aroma package but its not
>> >> >> > working
>> >> >> > with
>> >> >> > me , i don't know where is the error, and i have question the
>> >> >> > shiptype
>> >> >> > folder is not exist be default in annotationdata, i just
>> >> >> > create
>> >> >> > a
>> >> >> > folder in annotation data name it chiptype and i put the cdf file
>> >> >> > in
>> >> >> > it
>> >> >> > , is
>> >> >> > that possible ??? please i need your advice this is my program
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >>
>> >> >> Yes, that's what you should do. Here is some general advice that
>> >> >> could save you lots of time:
>> >> >>
>> >> >> 1. Read carefully the setup page:
>> >> >> http://www.aroma-project.org/setup,
>> >> >> and follow the links in that page.
>> >> >>
>> >> >> 2. Be really careful with the folder and file names:
>> >> >> "annotationData"
>> >> >> is not the same as "annotationdata", etc. The same holds for
>> >> >> function
>> >> >> names in the code you have pasted below, for example
>> >> >> "AffymetrixcdfFile" is not the same as "AffymetrixCdfFile", etc...
>> >> >>
>> >> >> 3. Do not try to guess/invent code lines if you are not familiar
>> >> >> with
>> >> >> the aroma framework. Instead, try to reproduce a vignette, for
>> >> >> example this one:
>> >> >> http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> Pierre
>> >> >>
>> >> >> >> getwd()
>> >> >> > [1]
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/ChipType"
>> >> >> >> ChipType(""HG-U133_Plus_2")
>> >> >> > Error: unexpected symbol in "ChipType(""HG"
>> >> >> >> ChipType("HG-U133_Plus_2")
>> >> >> > Error: could not find function "ChipType"
>> >> >> >> chipType("HG-U133_Plus_2")
>> >> >> > Error: could not find function "chipType"
>> >> >> >> library(aroma.affymetrix)
>> >> >> >> ChipeType("HG-U133_Plus_2")
>> >> >> > Error: could not find function "ChipeType"
>> >> >> >> chipType<-"HG-U133_Plus_2"
>> >> >> >> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2")
>> >> >> > Error: object 'AffymetrixcdfFile' not found
>> >> >> >> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2")
>> >> >> > Error: object 'AffymetrixcdfFile' not found
>> >> >> >> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2")
>> >> >> > Error: object 'AffymetrixcdfFile' not found
>> >> >> >> cdf<-HG-U133_Plus_2$bychipType("HG-U133_Plus_2")
>> >> >> > Error: object 'HG' not found
>> >> >> >> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2",
>> >> >> >> tags=ChipType)
>> >> >> > Error: object 'AffymetrixcdfFile' not found
>> >> >> >>
>> >> >> >
>> >> >> > the error is with cdf file which can not be read
>> >> >> > i download all the package
>> >> >> >
>> >> >> > source("http://bioconductor.org/biocLite.R";)
>> >> >> >
>> >> >> > biocLite("biomaRt")
>> >> >> >
>> >> >> > hbInstall("aroma.affymetrix")
>> >> >> >
>> >> >> > thank you
>> >> >> >
>> >> >
>> >> > --
>> >> > --
>> >> > 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-af...@googlegroups.com
>> >> > To unsubscribe and other options, go to
>> >> > http://www.aroma-project.org/forum/
>> >> >
>> >> > ---
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>> >> > "aroma.affymetrix" group.
>> >> > To unsubscribe from this group and stop receiving emails from it,
>> >> > send
>> >> > an
>> >> > email to aroma-affymetr...@googlegroups.com.
>> >> > For more options, visit https://groups.google.com/groups/opt_out.
>> >> >
>> >> >
>> >
>> > --
>> > --
>> > 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
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>> > To post to this group, send email to aroma-af...@googlegroups.com
>> > To unsubscribe and other options, go to
>> > http://www.aroma-project.org/forum/
>> >
>> > ---
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>> >
>> >
>
> --
> --
> 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
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> 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/
>
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>
--
--
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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