> getwd()
[1] "C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2"
*> chipType <- "HG-U133_Plus_2"*
*> chipTypeS <- gsub(",.*", "", chipType)*
*> path <- Arguments$getReadablePath(chipTypeS, path=pathAC, mustExist=TRUE)
*
*Error in getReadablePath.Arguments(static, ...) : *
* object 'pathAC' not found*
On Wednesday, May 1, 2013 1:22:08 PM UTC+1, nawin MOHAMMED wrote:
>
> I also tried put the cdf file in the HG-U133_Plus_2 folder directly
> as u see in the path but same error
> * > pathAC <- Arguments$getReadablePath("AromaAnalysis/HG-U133_Plus_2",
> mustExist=TRUE)*
>
> *[2013-05-01 13:20:42] Exception: Pathname not found:
> AromaAnalysis/HG-U133_Plus_2 (none of the parent directories
> [AromaAnalysis/] exist; current directory is
> 'C:/Users/nawin/AromaAnalysis/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$getReadablePath("AromaAnalysis/HG-U133_Plus_2",
> mustExist = TRUE)
> - Arguments$getReadablePath() is local of the calling function
>
> Error: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the
> parent directories [AromaAnalysis/] exist; current directory is
> 'C:/Users/nawin/AromaAnalysis/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'
> > getwd()
> [1] "C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2"
>
>
> On Wednesday, May 1, 2013 1:13:18 PM UTC+1, nawin MOHAMMED wrote:
>>
>>
>> Hi Henrik
>>
>>
>> i changed the directory as you told me but i got this error ??
>>
>> '
>> > pathAC <-
>> Arguments$getReadablePath("AromaAnalysis/ChipType/HG-U133_Plus_2",
>> mustExist=TRUE)
>> [2013-05-01 13:11:50] Exception: Pathname not found:
>> AromaAnalysis/ChipType/HG-U133_Plus_2 (none of the parent directories
>> [AromaAnalysis/ChipType/] exist; current directory is
>> 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2')
>>
>> at #05. getReadablePathname.Arguments(static, path = path, mustExist =
>> mustExist,
>> ...)
>> - getReadablePathname.Arguments() is in environment 'R.utils'
>>
>> at #04. getReadablePathname(static, path = path, mustExist = mustExist,
>> ...)
>> - getReadablePathname() is in environment 'R.utils'
>>
>> at #03. getReadablePath.Arguments(static, ...)
>> - getReadablePath.Arguments() is in environment 'R.utils'
>>
>> at #02. getReadablePath(static, ...)
>> - getReadablePath() is in environment 'R.utils'
>> - originating from '<text>'
>>
>> at #01.
>> Arguments$getReadablePath("AromaAnalysis/ChipType/HG-U133_Plus_2",
>> mustExist = TRUE)
>> - Arguments$getReadablePath() is local of the calling function
>>
>> Error: Pathname not found: AromaAnalysis/ChipType/HG-U133_Plus_2 (none of
>> the parent directories [AromaAnalysis/ChipType/] exist; current directory
>> is 'C:/Users/nawin/AromaAnalysis/ChipType/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'
>> > getwd()
>> [1] "C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2"
>> >
>>
>>
>> I don't know why that happen
>>
>> 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/
>>> >> >
>>> >> > ---
>>> >> > You received this message because you are subscribed to the Google
>>> >> > Groups
>>> >> > "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
>>> 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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>>> > To unsubscribe from this group and stop receiving emails from it, send
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>>> >
>>> >
>>>
>>
--
--
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