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$getReadablePath("annotationData/chipTypes/",
mustExist=TRUE)
[2013-05-01 15:31:49] Exception: Pathname not found:
annotationData/chipTypes (none of the parent directories [annotationData/]
exist; current directory is
'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2')
On Wednesday, May 1, 2013 1:34:30 PM UTC+1, Pierre Neuvial wrote:
>
> Hi,
>
> Please respect the people who are trying to help you out by not
> sending an email to the list every time you are trying a new (random)
> command, especially since you are not following the advice which is
> given to you.
>
> As Henrik suggested,
>
> 1. put "your data files (annotationData/, rawData/, etc.)" in
> "C:/Users/nwayyin/AromaAnalysis/"
>
> This means that you should have:
>
> "C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2"
>
> This is not what you have right now !
>
> and then, still quoting Henrik,
>
> 2. "let that be your working directory in R."
>
> This means that "getwd()" should say
>
> "C:/Users/nwayyin/AromaAnalysis"
>
> This is not what you did either !
>
> Please make sure that you did what has been suggested.
>
> Thanks,
>
> Pierre
>
> On Wed, May 1, 2013 at 2:27 PM, nawin MOHAMMED
> <naw...@gmail.com<javascript:>>
> wrote:
> >> getwd()
> > [1] "C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2"
> >> chipType <- "HG-U133_Plus_2"
> >> chipTypeS <- gsub(",.*", "", chipType)
> >> path <- Arguments$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<javascript:>
> > 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
> an
> > email to aroma-affymetr...@googlegroups.com <javascript:>.
> > 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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