[BioC] Exon array annotation with limma?

[raffaele.calogero at unito.it]

Dear Michael,

Since we are entering in the winter holiday and I have
some spare time, I will create a stand-alone function for
gene level annotation for exon-arrays using as input a
data frame, that can be generated by limma or other
statistical tools. it will be present in oneChannelGUI and
could be extracted from it without the need of installing
oneChannelGUI.

>On Wed, Dec 23, 2009 at 6:42 AM, Michael Imbeault
<michael.imbeault at sympatico.ca> wrote:

>    Hello Raffaele,

>    Interesting; do you think you could provide a package
to provide the same functionality that is >present in
oneChannelGUI (for gene-level annotation, that is)? I
looked at the code and it's a bit >interwined with
the onChannelGUI environment; is there an easy way to
extract the data frame and save >it as one external
to the environment in the mean-time?

In the mean time you can extract the anntoation data frame
generated from netaffx data using:
data("huex.annotation",package="oneChannelGUI") #for human
data("moex.annotation",package="oneChannelGUI")#for mouse
data("raex.annotation",package="oneChannelGUI")#for rat

In the latest release  of  oneChannelGUI (1.12.2 ,22
December 2009) of stable Bioconductor 2.5 you can find the
latest annotations released from Affymetrix in november.
Cheers
Raffaele


--
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
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email: raffaele.calogero at unito.it
         raffaele[dot]calogero[at]gmail[dot]com
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