[BioC] Converting gene names into Illumina IDs

Aliaksei Holik salvador at bio.bsu.by
Thu Sep 27 18:05:44 CEST 2012

Dear fellow Bioconductors,

I'm faced with a problem I can't get my head round and hope somebody 
would be able to point me in the right direction.

I am trying to plot a heatmap using expression values from my array for 
an external set of genes. I have used illuminaMousev2ALIAS2PROBE object 
to extract IlluminaIDs corresponding to the gene symbols in the set. 
Consistent with possibility of more than 1 probe per gene I got 1052 
IlluminaIDs for 510 gene names. However, if I try to remove duplicates I 
only get 259 IlluminaIDs, which makes no sense to me. I have checked and 
I do indeed get a lot of duplicated probe IDs. I wonder where I go 
wrong. Here's the code I used:

# Generate a list of gene symbols with corresponding Illumina IDs
xx <- as.list(illuminaMousev2ALIAS2PROBE)
# Subset all Illumina IDs for the genes present in SCSGenes vector
scs.probes.and.genes <- xx[SCSGenes]

# Generate a vector of probes while removing gene names
scs.probes <- as.character(unlist(scs.probes.and.genes))   #1058 probes
scs.probes <- na.omit(scs.probes)	 #1052 probes

# Remove duplicates
scs.probes <- scs.probes[!duplicated(scs.probes)] #259 probes
# end of code

Any help is much appreciated.

All the best,


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