[BioC] Mapping CDF from different array platforms

[Sean Davis]

On 8/10/05 5:15 PM, "Rifat Hamoudi" <rh335 at cam.ac.uk> wrote:

> Hello,
> Has anyone managed to compare data from different array platforms using R.
> If so what is the best way to do it. In particular I am doing the comparison
> of u95av2 with u133a. I am trying to do this by remapping the clones and
> creating new CDF using altcdfenvs package, but does anyone know of an easier
> way? I tried to use the Affy best match files ..etc but not sure if that is
> the perfect way to do it.

You could use biomaRt to get the mapping from Ensembl.  Starting with 10
affy Ids (you can easily use all of them) from the 133a chip, here is all
you need to do:

> a
 [1] "210256_s_at" "208608_s_at" "205536_at"   "200042_at"   "215167_at"
 [6] "219120_at"   "220890_s_at" "205111_s_at" "221370_at"   "201096_s_at"
> mart <- martConnect()
connected to:  ensembl_mart_32
> affy95 <- 
getXref(id=a,from.species='hsapiens',to.species='hsapiens',from.xref='affy_hg_u1
33a',to.xref='affy_hg_u95av2',mart=mart)
> affy95
An object of class "martTable"
Slot "id":
[1] "200042_at"   "201096_s_at" "205111_s_at" "205536_at"   "208608_s_at"
[6] "208608_s_at" "210256_s_at" "210256_s_at"

Slot "table":
$from.id
[1] "200042_at"   "201096_s_at" "205111_s_at" "205536_at"   "208608_s_at"
[6] "208608_s_at" "210256_s_at" "210256_s_at"

$to.id
[1] "38689_at" "36585_at" "40330_at" "1704_at"  "37074_at" "37075_at"
"31833_at"
[8] "39749_at"

$martID
[1] "ENSG00000100220" "ENSG00000168374" "ENSG00000138193" "ENSG00000160293"
[5] "ENSG00000172164" "ENSG00000172164" "ENSG00000143398" "ENSG00000180764"

Hope this helps.  

Sean