[BioC] HuGene annotation and htmls

[Mayte Suarez-Farinas]

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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>>
>>
>