Hi,
On Mon, Jun 18, 2012 at 5:39 PM, NT_CMU <[email protected]> wrote:
> Hi
>
> I am new to aroma.affymetrix. I am not sure why the command
> "AffymetrixCelSet$byName" is not working.
>
> cs <- AffymetrixCelSet$byName("test.CEL",chipType =
> "../../annotationData/chipTypes/GenomeWideSNP_6")
This will not work because
1- the first argument of 'AffymetrixCelSet$byName' should be the name
of your data set (this is why this function is called "byName"), as it
appears in your "rawData" folder. Is should not be a file name as
"test.CEL"
2- the 'chipType' argument should really be a chip type, e.g.
"GenomeWideSNP_6", not a path to a cdf file (as
"../../annotationData/chipTypes/GenomeWideSNP_6" is).
More below.
> Error in method(static, ...) :
> [2012-06-18 11:34:57] Exception: Failed to create AffymetrixCdfFile object.
> Could to locate an annotation data file for chip type
> '../../annotationData/chipTypes/GenomeWideSNP_6' (without requiring any
> tags) and with filename extension 'cdf'.
>
> at #04. method(static, ...)
> - method() is in environment 'aroma.core'
>
> at #03. AffymetrixCdfFile$byChipType(chipType)
> - AffymetrixCdfFile$byChipType() is local of the calling function
>
> at #02. method(static, ...)
> - method() is in environment 'aroma.affymetrix'
>
> at #01. AffymetrixCelSet$byName("test.CEL", chipType =
> "../../annotationData/chipTypes/GenomeWideSNP_6")
> - AffymetrixCelSet$byName() is local of the calling function
>
>
> I think my directory structure is wrong. But i could use some pointers on
> how to get things moving because i've been trying to get this command
> working for over 4 days now.
I don't know what your file structure is, can you describe it ?
Your file structure should match this one:
http://aroma-project.org/setup/QuickSummaryOfRequiredFileStructure
When you have that, you should be able to define an AffymetrixCelSet using
"AffymetrixCelSet$byName", for example
cs <- AffymetrixCelSet$byName("myDataSet",chipType="GenomeWideSNP_6")
where "myDataSet" is a character string containing the name of your
data set (not file names), and "GenomeWideSNP_6" is your chip type.
Important note: you should make sure that the working directory of
your R session contains "annotationData", "rawData", etc.
Is that the case for you ?
Cheers,
Pierre
PS (quoting Henrik): "If you find yourself specifying paths or full
pathname in your main
aroma.affymetrix scripts, you are doing something wrong. The package
is design to work without having to specify paths. A rule of thumb is
that you should be able to move any aroma.affymetrix script to another
computer system and run it without having to change anything." [thread
'How do you analyze Gene ST Data?', Oct 21, 2008].
>
> Also, another issue is I am able to load CDF files with the basic
> "AffymetrixCdfFile("GenomeWideSNP_6,Full.CDF") ". But if i use the command
> AffymetrixCdfFile$byChipType("GenomeWideSNP_6",tags="Full"), it gives me an
> error. Am I doing something really wrong?
>
> Thanks
>
> Nitesh
>
>
> --
> 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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--
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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