what is this ??? mean
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'
On Wednesday, May 1, 2013 3:39:10 PM UTC+1, nawin MOHAMMED wrote:
>
> Iam so sorry thank u and i am grateful , but iam just trying solve my
> error .??
> and this is also not working again , ok \i create a folder in
> user\nwayyin\ the name is (AromaAnalysis) then i create another folder
> with name annotationData then another folder with HG-U133_Plus_2
> which contain CDF file as bellow :
>
>
> > getwd()
> [1] "C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2"
> > library("R.utils")
> > pathAC <- Arguments$getReadablePath("annotationData/chipTypes/",
> mustExist=TRUE)
> [2013-05-01 15:31:49] Exception: Pathname not found:
> annotationData/chipTypes (none of the parent directories [annotationData/]
> exist; current directory is
> 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2')
>
>
>
>
> On Wednesday, May 1, 2013 1:34:30 PM UTC+1, Pierre Neuvial wrote:
>>
>> Hi,
>>
>> Please respect the people who are trying to help you out by not
>> sending an email to the list every time you are trying a new (random)
>> command, especially since you are not following the advice which is
>> given to you.
>>
>> As Henrik suggested,
>>
>> 1. put "your data files (annotationData/, rawData/, etc.)" in
>> "C:/Users/nwayyin/AromaAnalysis/"
>>
>> This means that you should have:
>>
>> "C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2"
>>
>> This is not what you have right now !
>>
>> and then, still quoting Henrik,
>>
>> 2. "let that be your working directory in R."
>>
>> This means that "getwd()" should say
>>
>> "C:/Users/nwayyin/AromaAnalysis"
>>
>> This is not what you did either !
>>
>> Please make sure that you did what has been suggested.
>>
>> Thanks,
>>
>> Pierre
>>
>> On Wed, May 1, 2013 at 2:27 PM, nawin MOHAMMED <naw...@gmail.com> wrote:
>> >> getwd()
>> > [1] "C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2"
>> >> chipType <- "HG-U133_Plus_2"
>> >> chipTypeS <- gsub(",.*", "", chipType)
>> >> path <- Arguments$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
>> > "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
>> 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.
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