I'm trying to parse the probe set ids from the file 'GSE15543' ,the GDS file name of the same study is GDS4027.
There is a problem while parsing the probe ids from GSE.
fData(eset2)[nrow(fData(eset)),] #nrow = 54675
ID GB_ACC SPOT_ID Species Scientific Name Annotation Date Sequence Type NA.41561 <NA> <NA> <NA> <NA> <NA> <NA> Sequence Source Target Description Representative Public ID Gene Title NA.41561 <NA> <NA> <NA> <NA> Gene Symbol ENTREZ_GENE_ID RefSeq Transcript ID Gene Ontology Biological Process NA.41561 <NA> <NA> <NA> <NA> Gene Ontology Cellular Component Gene Ontology Molecular Function NA.41561
gds <- getGEO('GDS4027')
eset = GDS2eSet(gds)
fData(eset)[nrow(fData(eset)),] #nrow = 54675
ID Gene title Gene symbol Gene ID UniGene title AFFX-TrpnX-M_at AFFX-TrpnX-M_at UniGene symbol UniGene ID Nucleotide Title GI GenBank Accession AFFX-TrpnX-M_at NA Platform_CLONEID Platform_ORF Platform_SPOTID Chromosome location AFFX-TrpnX-M_at --Control Chromosome annotation GO:Function GO:Process GO:Component GO:Function ID AFFX-TrpnX-M_at GO:Process ID GO:Component ID AFFX-TrpnX-M_at
As displayed in the above outputs, I am not able to obtain the probe id while using the expression set created using gse file.
In short, the trouble is
> rownames(exprs(eset2))  "1007_s_at" > rownames(exprs(eset2))  "NA.41561"
I'm not able to parse all the probe ids (e.g "NA.41561") and therefore not able to map these to gene symbols.
I would like to parse all the probe set ids from the gse file, map the probe ids to the gene symbols. Any help will be much appreciated.