Question: Mapping CDF from different array platforms
0
13.9 years ago by
Rifat Hamoudi30 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. Thanks Rifat
cdf affy altcdfenvs • 493 views
modified 13.9 years ago by Sean Davis21k • written 13.9 years ago by Rifat Hamoudi30
Answer: Mapping CDF from different array platforms
0
13.9 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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