[BioC] Human Gene 1.0 ST array

[Marc Carlson]

Just going by the error message, you will also need the development
version of AnnotationDbi.  Although I think Jim's point was that it
would be good to just upgrade everything, which is great advice since
that is how these things are tested (ie. within a release).

  Marc



James W. MacDonald wrote:
> Hi Chandra,
>
> Chandra Sekhar wrote:
>> Hi,
>>
>> I would like to extract gene names (featureNames) using annaffy, but
>> i am unable to
>> find Affymetrix probe sequence and annotation data for Human Gene 1.0
>> ST array. Installed
>> bioconductor version 2.2 and R version 2.7.2.
>>
>> I tried below link (2.3 devel), apparently it gives Error:
>> AnnotationDbi version is 1.2.2 , >= 1.3.x
>> is needed by hugene10st
>
> Yes. If you want to use the devel version of BioC, you need to use the
> devel version of R. Since both will be released within weeks, there is
> really no reason not to upgrade.
>
> Best,
>
> Jim
>
>
>>
>> http://www.bioconductor.org/packages/2.3/data/annotation/html/hugene10st.db.html
>>
>>
>> (CEL files belonging to human gene 1.0 st array)
>> rawdata<-ReadAffy()
>> symbols<-aafSymbol(featureNames(rawdata),"hugene10st.db")
>>
>> I could successfully perform the same operation using Affymetrix Human
>> Genome U133 Plus 2.0 Array
>> (CEL files belonging to U133)
>>
>> symbols<-aafSymbol(featureNames(rawdata),"hgu133plus2")
>>
>> Please let me know if Human gene 1.0 ST array is supported.
>>
>> Thanks,
>> Chandra
>>
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>