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 
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>> > To unsubscribe from this group and stop receiving emails from it, send 
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>> > email to aroma-affymetr...@googlegroups.com. 
>> > For more options, visit https://groups.google.com/groups/opt_out. 
>> > 
>> > 
>>
>

-- 
-- 
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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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