[BioC] HuGene annotation and htmls

[James W. MacDonald]

I wonder if this is a problem with how the package was built. The 
numbers that Marc supplied are the Exon Probeset IDs, but the Lkeys of 
the hugene10st.db package seem to be what Affy calls the Transcript 
Cluster ID.

 > keys <- c("7903188","7903203")
 > getSYMBOL(keys, "hugene10st")
7903188 7903203
"PTBP2"  "SNX7"

Best,

Jim



Mayte Suarez-Farinas wrote:
> I meant that the usual functions from annotate does not work.
> When I ran your code, I get:
> 
> library("annotate")
>  > library("hugene10st.db")
>  > keys = c("7903193","7903204")
>  >
>  > getSYMBOL(keys, "hugene10st")
> 7903193 7903204
>      NA      NA
>  >
>  > lookUp(keys, "hugene10st" , "CHR")
> $`7903193`
> [1] NA
> 
> $`7903204`
> [1] NA
> 
>  > lookUp(keys, "hugene10st" , "ENTREZID")
> $`7903193`
> [1] NA
> 
> $`7903204`
> [1] NA
> 
> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     
> datasets  methods   base
> 
> other attached packages:
>  [1] hugene10st.db_1.0.2  statmod_1.3.8        beadarray_1.10.0     
> sma_0.5.15           hwriter_1.0
>  [6] affycoretools_1.14.1 annaffy_1.14.0       KEGG.db_2.2.5        
> biomaRt_1.16.0       GOstats_2.8.0
> [11] Category_2.8.4       RBGL_1.18.0          GO.db_2.2.5          
> RSQLite_0.7-1        DBI_0.2-4
> [16] graph_1.20.0         limma_2.16.4         affyQCReport_1.20.0  
> geneplotter_1.20.0   annotate_1.20.1
> [21] AnnotationDbi_1.5.18 lattice_0.17-17      RColorBrewer_1.0-2   
> affyPLM_1.18.1       preprocessCore_1.4.0
> [26] xtable_1.5-4         simpleaffy_2.18.0    gcrma_2.14.1         
> matchprobes_1.14.1   genefilter_1.22.0
> [31] survival_2.34-1      affy_1.20.2          Biobase_2.2.2
> 
> loaded via a namespace (and not attached):
> [1] GSEABase_1.4.0     KernSmooth_2.22-22 RCurl_0.94-1       
> XML_2.1-0          affyio_1.10.1
> [6] cluster_1.11.11    grid_2.8.1         xps_1.2.8
> 
> 
> On Apr 9, 2009, at 5:26 PM, Marc Carlson wrote:
> 
>> Hi Mayte,
>>
>> I can't tell from your post what you tried to do, or even what exactly
>> you need to know.  Please give us the code you were trying to use, along
>> with an example that didn't behave the way you expected it to and you
>> the results of calling sessionInfo() after you did that. You can find
>> other helpful tips on the posting guide:
>>
>> http://www.bioconductor.org/docs/postingGuide.html
>>
>> What little I can discern from your post I will try to answer.  To use
>> getSYMBOL() or lookUp(), you need to 1st of all make sure that you have
>> loaded the annotate package.  Then you need to call it correctly.  Here
>> is an example that I did using the very latest version of the
>> hugene10st.db package.
>>
>> library("annotate")
>> library("hugene10st.db")
>> keys = c("7903193","7903204")
>>
>> getSYMBOL(keys, "hugene10st")
>>
>> lookUp(keys, "hugene10st" , "CHR")
>> lookUp(keys, "hugene10st" , "ENTREZID")
>>
>>
>>
>> Hope this helps,
>>
>>
>>
>>   Marc
>>
>>
>>
>>
>>
>>
>> Mayte Suarez-Farinas wrote:
>>> I am learning to work with the HuGene ST1 chips.
>>> I was able to use xps to read and preprocess the files
>>> and then I convert to ExpressionSet class to use limma
>>> for modelling.
>>> Next step I stop: the annotation.
>>> I load  library("hugene10st.db") but the normal functions
>>> to create html annotation does not seems to work on this chip.
>>> I also try to get each component using getSYMBOL and lookUP
>>> with no success.
>>> what's the way to go???
>>>
>>> Thanks
>>>
>>> Mayte
>>>
>>>
>>>
>>>
>>>
>>>     [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
>>>
>>
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826