[BioC] mapping gene name to affy id

[Mark Robinson]

Raphael.

What if you 'filter' on the 'value' you are looking for, such as:

 >  
getBM 
(attributes 
=c("affy_hg_u133_plus_2","hgnc_symbol","chromosome_name","band"),
                      filters="hgnc_symbol",values="CD86", mart=mart)

   affy_hg_u133_plus_2 hgnc_symbol chromosome_name   band
1           205685_at        CD86               3 q13.33
2         210895_s_at        CD86               3 q13.33
3         205686_s_at        CD86               3 q13.33

Cheers,
Mark


 > sessionInfo()
R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1

locale:
en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_1.16.0

loaded via a namespace (and not attached):
[1] RCurl_0.91-0 XML_1.98-1




On 08/12/2008, at 8:37 AM, Ruppert Valentino wrote:

>
>
> Hello,
>
> I wonder if anyone has come across the same problem as I am having.
>
> I am trying to map a gene name i.e HGNC symbol to its corresponding  
> affymetrix probe using R/Bioconductor but I don't seem to be able to  
> do it using biomaRt
>
> I tried :
>
> getBM 
> (attributes 
> = 
> c 
> ("affy_hg_u133_plus_2 
> ","hgnc_symbol 
> ","chromosome_name 
> ","band"),filters="affy_hg_u133_plus_2",values="CD86", mart=mart)
>
> and other similar code but they don't work
>
> The previous version of biomaRt that uses getFeature() worked when I  
> use something like this :
>
> feat = getFeature(symbol = "CD86", type = "affy_hg_u133_plus_2",  
> mart = mart)
>
> but I just can't seem to get the same to work using getBM which now  
> superceeds getFeature
>
> has anyone come across the same problem and if so how did they solve  
> it.
>
> Many thanks.
>
> Raphael.
>
>
> _________________________________________________________________
> Get a bird’s eye view of the world with Multimap
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852