Hi.
On Tue, Nov 15, 2011 at 1:23 PM, Michelle <suyi...@gmail.com> wrote:
> Hi Henrik,
> I downloaded the acs annotation file and now the code works for this 250K
> dataset. However, for my SNP 6.0 data, I still get this error message
> "Exception: Could not locate a file for this chip type: GenomeWideSNP_6"
> Under annotation directory I have these files:
> GenomeWideSNP_6,Full,monocell.CDF
> GenomeWideSNP_6,Full.cdf
> GenomeWideSNP_6,HB20080710.acs
> GenomeWideSNP_6,Full,na26,HB20080722.ufl
> GenomeWideSNP_6,Full,na26,HB20080821.ugp
> GenomeWideSNP_6,na31,hg19,HB20110328.ufl
> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
The GenomeWideSNP_6 (and the GenomeWideSNP_5) chip is special, because
Affymetrix provides two different *annotation* sets (CDFs), one
"default" and one "full".
To use the "Full" annotation, you need the following annotation data files:
GenomeWideSNP_6,HB20080710.acs (same for "default" and "full")
GenomeWideSNP_6,Full.cdf
GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
and then do:
dataSet <- "TCGABreast";
chipType <- "GenomeWideSNP_6,Full";
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
...
/Henrik
>
> and the output is
>> library("aroma.affymetrix");
>>
>> cwd="C:/Data/TCGA/_aroma_/"
>> setwd(cwd)
>>
>> dataSet <- "TCGABreast";
>> chipType <- "GenomeWideSNP_6";
>>
>> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
> Error in list(`AffymetrixCelSet$byName(dataSet, chipType = chipType)` =
> <environment>, :
>
> [2011-11-15 16:16:21] Exception: Could not locate a file for this chip type:
> GenomeWideSNP_6
> at throw(Exception(...))
> at throw.default("Could not locate a file for this chip type: ",
> paste(c(chipType, tags), collapse = ","))
> at throw("Could not locate a file for this chip type: ", paste(c(chipType,
> tags), collapse = ","))
> at method(static, ...)
> at AffymetrixCdfFile$byChipType(chipType)
> at method(static, ...)
> at AffymetrixCelSet$byName(dataSet, chipType = chipType)
>
> --
> 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
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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.
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/
