You are right James!!!
with the keys James  sent the package hugene10st  work just fine.
so it looks like the "error" come from my use of xps.

here is my code:

library(xps)

### define directories:
# directory containing Affymetrix library files
libdir <- "/Users/Mayte/Rlibrary/AffyDB/libraryfiles"
anndir <- "/Users/Mayte/Rlibrary/AffyDB/Annotation"
scmdir <- "/Users/Mayte/Rlibrary/AffyDB/ROOTSchemes"

scheme.hugene10stv1r4.na28 <- import.exon.scheme 
("Scheme_HuGene10stv1r4_na28",filedir=scmdir,
                               layoutfile=paste(libdir,"HuGene-1_0-st- 
v1.r4.clf",sep="/"),
                               schemefile=paste(libdir,"HuGene-1_0-st- 
v1.r4.pgf",sep="/"),
                               probeset=paste(anndir,"HuGene-1_0-st- 
v1.na28.hg18.probeset.csv",sep="/"),
                               transcript=paste(anndir,"HuGene-1_0-st- 
v1.na28.hg18.transcript.csv",sep="/"))

scheme.hugene10stv1r4 <- root.scheme(paste(scmdir,  
"Scheme_HuGene10stv1r4_na28.root",sep = "/"))
G1ST_data<-import.data(scheme.hugene10stv1r4, "Pamela_G1ST_dataxps",  
celdir=getwd(), celfiles = as.character(PD[1:8,'CELfile']), verbose =  
FALSE)
G1ST_rma_xps <- rma(G1ST_data, "Pamela_G1ST_rma_t",  
background="antigenomic", option="transcript", exonlevel="core+affx",  
normalize=T)

The "featureNames" of the data (or keys) can be  taken as:

keys<-as.character(exprs(G1ST_rma_xps)$UnitName)

but almost half them do not have symbol:

sum(!is.na(getSYMBOL(keys, "hugene10st")))
[1] 19899
sum(is.na(getSYMBOL(keys, "hugene10st")))
  9027

Is this OK ? or is there any mistake in my code??

Thanks in advance for everybody help!!!
and sorry for bothering so many times!

Mayte

On Apr 10, 2009, at 10:55 AM, James W. MacDonald wrote:

> 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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>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives: http://news.gmane.org/ 
>>>> gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/ 
>> gmane.science.biology.informatics.conductor
>
> -- 
> 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


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