Alex Tsoi wrote:
> Dear all,
>
> I am trying to get ALL the gene names (symbol) and their
corresponding locus
> link ID from around 10 different Affymetrix platforms, but I am not
quite
> sure how to do that.....effeciently.
>
> I know I could use the aafSymbol from the annaffy package or the
getLL /
> getSYMBOL from the annotate package to do that, but all of these
functions
> require to input a set of identifiers (the probesets), and in my
case, I
> will have to get ALL the probesets from my experiment first, and
then call
> the function to get all the Locus Link id / symbol corresponding to
that
> chip.
>
> Do you guys have some more effecient ways to retrieve all the locus
link id
> or the symbol from different affymetrix platforms ? I greatly
appreciate for
> the help.
>
> Thanks a lot,
>
>
You could use the LL Mappings packages. The only catch is that then
you
will have all the entrez gene IDs which would go well beyond your
current ten platforms. We don't have a list of all the probesets from
your ten platforms, so we can only meet you halfway on this. ;)
Marc
>
>I am trying to get ALL the gene names (symbol) and their
corresponding locus
>link ID from around 10 different Affymetrix platforms, but I am not
quite
>sure how to do that.....effeciently.
>
>I know I could use the aafSymbol from the annaffy package or the
getLL /
>getSYMBOL from the annotate package to do that, but all of these
functions
>require to input a set of identifiers (the probesets), and in my
case, I
>will have to get ALL the probesets from my experiment first, and then
call
>the function to get all the Locus Link id / symbol corresponding to
that
>chip.
>
>Do you guys have some more effecient ways to retrieve all the locus
link id
>or the symbol from different affymetrix platforms ? I greatly
appreciate for
>the help.
Is this what you want?
>lilbrary(hgu95av2)
>geneNames <- mget(ls(hgu95av2SYMBOL), hgu95av2SYMBOL)
>
>Thanks a lot,
>
>--
>Lam C. Tsoi (Alex)
>Medical University of South Carolina
>
> [[alternative HTML version deleted]]
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
