From Microarray to RNASeq

Question

[rbrtdambrosio]

Hello, I'm looking for a way to map the probesets from HGU133plus 2.0 platform to the corresponding gene symbols or LocusLinks (that is the annotation used in TCGA). Which is the correct way to do the mapping?

Thanks

Answer 1

[dariober]

What about using biomaRt? Something like this, change as appropriate:

library(biomaRt)
mart<- useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "dec2015.archive.ensembl.org", dataset= 'hsapiens_gene_ensembl')

listAttributes(mart) ## Choose from these
affy<- getBM(attributes= c('affy_hg_u133_plus_2', 'ensembl_gene_id', 'external_gene_name'), mart= mart)

affy[affy$affy_hg_u133_plus_2 != '',][1:10,]
   affy_hg_u133_plus_2 ensembl_gene_id external_gene_name
6         1553551_s_at ENSG00000198888             MT-ND1
7         1553551_s_at ENSG00000210100              MT-TI
9         1553551_s_at ENSG00000210112              MT-TM
10        1553551_s_at ENSG00000198763             MT-ND2
16          1553569_at ENSG00000198804             MT-CO1
17        1553538_s_at ENSG00000198804             MT-CO1
18        1553570_x_at ENSG00000198804             MT-CO1
20          1553569_at ENSG00000210154              MT-TD
21        1553570_x_at ENSG00000210154              MT-TD
22          1553569_at ENSG00000198712             MT-CO2

[rbrtdambrosio]

Thanks for the reply. I have already tried biomart but I wasn't completely satisfied with the results that I obtained. Ad examples it mapped the probeset 204960_at to CORO1B and PTPRCAP. While using the probeset sequence in Blast, the only result is PTPRCAP. So I'm looking for a more reliable solution.