Is the same probeset_id and transcript_cluster_id in HuGene-1_0-st-v1 ?

Question

[64bga]

Hi everybody,

I'm new in microarrays analysis and I have some HuGene-1_0-st-v1 .CEL files and when I use BioMart to convert HuGene-1_0-st-v1 probeset to Ensembl gene Id, my probeset_id's don't appear in Ensembl_gene_Id, but if I use transcript_cluster_id I get the results. For example:

Affy HuGene 1_0 st v1 probeset(But this ID is my transcript_cluster_id)     Ensembl Transcript ID
                        7896736                                                                          ENST00000598977
                        7896736                                                                          ENST00000594647

But If I introduce the "real" probeset_id I get NO DATA

I have some troubles to distinguish the information about the probeset.csv and transcript.csv to read the annotation

thanks in advance!!

Answer 1

[cqtnljy]

64bga,

I suggest you use biomaRt package of R to convert HuGene-1_0-st-v1 probeset ids to Ensembl gene IDs.

source("http://bioconductor.org/biocLite.R")
biocLite('biomaRt")
library(biomaRt)
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
getBM(attributes=c('affy_hugene_1_0_st_v1', 'hgnc_symbol'),filters="affy_hugene_1_0_st_v1",value="xxxx",mart=ensembl)# value:your probeset id