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<javascript:>>
> 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-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.
