[BioC] gene level on exon chip?

[cstrato]

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_US.UTF-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_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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>
>