[aroma.affymetrix] Trying to create a CDF file from an R package/environment problems

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[aroma.affymetrix] Trying to create a CDF file from an R package/environment problems

Fong
Hi,

I've found a set of R packages (CDF) files from a service called
GATExplorer (http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?
content=rprogram) and I am trying to create a CDF file from the R
packages.  I've followed the instructions found at http://www.aroma-project.org/node/41
but I am running to errors.  This is what happens:

Env2Cdf("genemapperhgu133plus2cdf", "u1332plus_ivt_breast_A.CEL",
overwrite=TRUE)
Loading required package: affxparser
Reading environment: genemapperhgu133plus2cdf.
Reading CEL file header.
Creating CDF list for 20172 units.
Error in FUN(X[[1L]], ...) : no 'dimnames' attribute for array

I am not too familiar with how CDF R packages work.  Does anyone have
any advice on what I could do?

Thanks,

Fong

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[aroma.affymetrix] Re: Trying to create a CDF file from an R package/environment problems

Fong
For those interested I got a reply from the makers of the CDF files
and apparently it is an issue on their end.  Here is their reply:

We have been studying the problem and we have discovered a bug in
perfect match and mismatch probes annotation that makes Env2Cdf
function unable to use packages from GATExplorer.

We send you GeneMapper and TranscriptMapper for HG_U133_Plus2
with the bug corrected. In a couple of days we will upload all
the packages to GATExplorer website.

Looks like it was an issue on their end.

On Oct 12, 12:48 pm, Fong <[hidden email]> wrote:

> Hi,
>
> I've found a set of R packages (CDF) files from a service called
> GATExplorer (http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?
> content=rprogram) and I am trying to create a CDF file from the R
> packages.  I've followed the instructions found athttp://www.aroma-project.org/node/41
> but I am running to errors.  This is what happens:
>
> Env2Cdf("genemapperhgu133plus2cdf", "u1332plus_ivt_breast_A.CEL",
> overwrite=TRUE)
> Loading required package: affxparser
> Reading environment: genemapperhgu133plus2cdf.
> Reading CEL file header.
> Creating CDF list for 20172 units.
> Error in FUN(X[[1L]], ...) : no 'dimnames' attribute for array
>
> I am not too familiar with how CDF R packages work.  Does anyone have
> any advice on what I could do?
>
> Thanks,
>
> Fong

--
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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Re: [aroma.affymetrix] Re: Trying to create a CDF file from an R package/environment problems

Henrik Bengtsson-4
Thanks for follow up/reporting back to the list.

/Henrik

On Thu, Oct 14, 2010 at 12:03 PM, Fong <[hidden email]> wrote:

> For those interested I got a reply from the makers of the CDF files
> and apparently it is an issue on their end.  Here is their reply:
>
> We have been studying the problem and we have discovered a bug in
> perfect match and mismatch probes annotation that makes Env2Cdf
> function unable to use packages from GATExplorer.
>
> We send you GeneMapper and TranscriptMapper for HG_U133_Plus2
> with the bug corrected. In a couple of days we will upload all
> the packages to GATExplorer website.
>
> Looks like it was an issue on their end.
>
> On Oct 12, 12:48 pm, Fong <[hidden email]> wrote:
>> Hi,
>>
>> I've found a set of R packages (CDF) files from a service called
>> GATExplorer (http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?
>> content=rprogram) and I am trying to create a CDF file from the R
>> packages.  I've followed the instructions found athttp://www.aroma-project.org/node/41
>> but I am running to errors.  This is what happens:
>>
>> Env2Cdf("genemapperhgu133plus2cdf", "u1332plus_ivt_breast_A.CEL",
>> overwrite=TRUE)
>> Loading required package: affxparser
>> Reading environment: genemapperhgu133plus2cdf.
>> Reading CEL file header.
>> Creating CDF list for 20172 units.
>> Error in FUN(X[[1L]], ...) : no 'dimnames' attribute for array
>>
>> I am not too familiar with how CDF R packages work.  Does anyone have
>> any advice on what I could do?
>>
>> Thanks,
>>
>> Fong
>
> --
> 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 [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
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/.
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