[BioC] [Fwd: Re: gene level on exon chip?]

[Steve Piccolo]

Hi Paul,

This article may also be of interest: "Exon arrays provide accurate
assessments of gene expression" (http://genomebiology.com/2007/8/5/R82).
Though it doesn't look like they have an R implementation.

Regards,
-Steve

----------------------------------------------------------------
Stephen Piccolo

PhD Student
Department of Biomedical Informatics, University of Utah
Salt Lake City, UT 84112-5750

My Informatics Blog: http://biomedicalinformatics.wordpress.com
-----------------------------------------------------------------

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of cstrato
Sent: Friday, April 18, 2008 4:57 AM
To: Paul Hammer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] [Fwd: Re: gene level on exon chip?]

Dear Paul

Please let me comment on Michal's warning:
Even the Affymetrix people claim that you can use the exon arrays
to compute gene expression levels, however, I agree with Michal
that you must be careful. Affymetrix has divided the probesets into
(meta)core, extended and full. If you select only (meta)core (which
you can do with xps) then my experience shows that you are on the
save side.

Since you want to compare your results with gene chips, Affymetrix
provides "BestMatch" files for this purpose. The following paper
of Robinson & Speed, who compare HuExon to HuGene and
HGU133plus2 arrays may also be of interest to you:
http://www.biomedcentral.com/1471-2105/8/449

Best regards
Christian


Paul Hammer wrote:
>
>
>
------------------------------------------------------------------------
>
> Subject:
> Re: [BioC] gene level on exon chip?
> From:
> Paul Hammer <Paul.Hammer at p-t-p.de>
> Date:
> Thu, 17 Apr 2008 16:56:37 +0200
> To:
> Michal Okoniewski <michal.okoniewski at fgcz.ethz.ch>
>
> To:
> Michal Okoniewski <michal.okoniewski at fgcz.ethz.ch>
>
>
> Michal Okoniewski schrieb:
>> Just a small warning Paul... There is no such thing as "gene level" 
>> expression, especially with exon chips.
>> There are various affinities, various amount of intronic and exonic 
>> probes within a gene and possible splicing of course.
>> You can run gene level summarization with Christian's tool or with 
>> Brainarray CDF, but think of the
>> interpretation - if it exists. Alternatively/complementarily I would 
>> eg. plot all your genes of interest in exonmap.
>>
>> Best,
>> Michal
>>
>> Paul Hammer wrote:
>>> hi members,
>>>
>>> is there any function or easy way to get the gene level of a human 
>>> exon affymetrix chip? currently i calculate the average of all 
>>> exonic probeset intensities for genes of interest individually.
>>>
>>> other question what i have is there any easy way to remove poor 
>>> performing probesets via DABG (detection above background score)?
>>>
>>> many thanks and best regards
>>> paul
>>>
>>>
>>>  > sessionInfo()
>>> R version 2.6.2 (2008-02-08)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>>
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID
ENTIFICATION=C 
>>>
>>>
>>> attached base packages:
>>> [1] splines   tools     stats     graphics  grDevices utils     
>>> datasets
>>> [8] methods   base
>>>
>>> other attached packages:
>>>  [1] exonmap_1.4.3        plier_1.8.0          RMySQL_0.6-0
>>>  [4] DBI_0.2-4            RColorBrewer_1.0-2   simpleaffy_2.14.05
>>>  [7] gcrma_2.10.0         matchprobes_1.10.0   genefilter_1.16.0
>>> [10] survival_2.34        affy_1.16.0          preprocessCore_1.0.0
>>> [13] affyio_1.6.1         Biobase_1.16.3
>>>
>>> loaded via a namespace (and not attached):
>>> [1] annotate_1.16.1     AnnotationDbi_1.0.6 rcompgen_0.1-17
>>> [4] RSQLite_0.6-8
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: 
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>   
>>
> first thanks for help...
>
> @ Christian and Mark: i have installed both packages just now. lets 
> see which is my favorite :)
>
> @ michal: you are absolutely right. i know only to well how hard it is

> to interpret gene levels on exon chips. but i try to compare results 
> from exon chips with gene chips. by the way how are you calculating 
> the gene level within the function splicing.index()?
>
> cheers
> paul
>
>
>
>
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