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<javascript:>>
> 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<javascript:>
> > 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 <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.
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-affymetrix@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-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
