Hi,

Please respect the people who are trying to help you out by not
sending an email to the list every time you are trying a new (random)
command, especially since you are not following the advice which is
given to you.

As Henrik suggested,

1. put "your data files (annotationData/, rawData/, etc.)" in
"C:/Users/nwayyin/AromaAnalysis/"

This means that you should have:

 "C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2"

This is not what you have right now !

and then, still quoting Henrik,

2. "let that be your working directory in R."

This means that "getwd()" should say

"C:/Users/nwayyin/AromaAnalysis"

This is not what you did either !

Please make sure that you did what has been suggested.

Thanks,

Pierre

On Wed, May 1, 2013 at 2:27 PM, nawin MOHAMMED <nawi...@gmail.com> wrote:
>> 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/
>>>> >
>>>> > ---
>>>> > 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
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>
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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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