Hi wisekh6,
Although you don't give the code you used to process this data, from
what you report it looks like you initially processed your data set
using the "full" chip type. See below.
On Fri, Nov 11, 2011 at 7:22 AM, wisekh6 <wise...@gmail.com> wrote:
> Dear all,
>
> After processing Affymetrix GenomeWide SNP 6.0, I wanted to access
> 'chip effect data set' by using:
> cesN <- CnChipEffectSet$byName("AffyTestData",tags="ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY", chipType="GenomeWideSNP_6")
>
> But, it failed, generating an error message: can't locate...
Here you try to retrieve the data set as if it had been processed
using the standard (ie non "full") chip type, and apparently it was
not the case.
>
> Using the following command successfully worked:
> cesN <- CnChipEffectSet$byName("AffyTestData",tags="ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY", chipType="GenomeWideSNP_6,Full")
>
This one works because what you ask to retrieve corresponds to what
you did initially.
> The only difference is that the latter command used
> "GenomeWideSNP_6,Full" as chipType rather than "GenomeWideSNP_6."
>
> Does anyone let me know why the former command failed to work?
> Originally, I believed that the former command would be correct.
As explained above, both commands are "correct", but the first one
cannot retrieve what you ask because the corresponding processed data
set does not exist.
>
> FYI: The corresponding annotation file is in the following directory:
> annotationData\chipTypes\GenomeWideSNP_6
>
>
> Thank you.
>
I hope this helps,
Pierre
>
> --
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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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