[BioC] Converting gene names into Illumina IDs

[Aliaksei Holik]

Before anyone replies, I just had an idea that I should try 
illuminaMousev2SYMBOL instead of illuminaMousev2ALIAS2PROBE. If I fail, 
in that I'll send another e-mail.

Thanks again.

On 27/09/2012 17:05, Aliaksei Holik wrote:
> 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,
>
> Aliaksei.
>
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