[BioC] gene level on exon chip?

[Mark Robinson]

Hi Paul.

Another option is the 'aroma.affymetrix' package:
http://groups.google.com/group/aroma-affymetrix

Specifically, have a look at:
http://groups.google.com/group/aroma-affymetrix/web/human-exon-array- 
analysis
... there is a section called "Summarization" which talks about  
getting gene-level (or probeset-level) summaries.

Taking averages of probeset summaries should perform very badly.

Cheers,
Mark


On 16/04/2008, at 7:38 AM, cstrato wrote:

> Dear Paul
>
> For example, my package "xps" (available from BioC 2.2) is able to
> calculate normalized expression levels of exon arrays both at the gene
> level and at the probeset level. In addition, it can compute DABG  
> calls
> also on the gene level and probeset level. You are even able to  
> compute
> MAS5 calls for the exon arrays and compare the results to the DABG  
> calls.
>
> I hope this info is helpful.
> Best regards
> Christian
> _._._._._._._._._._._._._._._._
> C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
> V.i.e.n.n.a       A.u.s.t.r.i.a
> e.m.a.i.l:    cstrato at aon.at
> _._._._._._._._._._._._._._._._
>
>
> 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_U 
>> S.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U 
>> S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT 
>> F-8;LC_IDENTIFICATION=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
>>
>> _______________________________________________
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>>
>>
>
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