On Mon, Jun 18, 2012 at 1:59 PM, NT_CMU <[email protected]> wrote:
> Hi
>
> Thanks for the help Pierre. I managed to resolve it. I am just using the
> AffymetrixCelSet$byName with the cdf information instead of the chipType.
> For some reason, that still refuses to work.
These are the two possible ways to setup the CEL data set:
cs <- AffymetrixCelSet$byName("LeeAV_2012", chipType="GenomeWideSNP_6,Full")
and
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
cs <- AffymetrixCelSet$byName("LeeAV_2012", cdf=cdf);
and it appears from you file listing that that should be the case for
you. If you get both to work, you've ready to move on.
/Henrik
>
> Nitesh
>
>
> On Monday, 18 June 2012 11:39:34 UTC-4, NT_CMU 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")
>> 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.
>>
>> 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
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--
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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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