[BioC] gene level on exon chip?
cstrato at aon.at
Tue Apr 15 23:38:53 CEST 2008
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.
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
> > sessionInfo()
> R version 2.6.2 (2008-02-08)
> attached base packages:
>  splines tools stats graphics grDevices utils datasets
>  methods base
> other attached packages:
>  exonmap_1.4.3 plier_1.8.0 RMySQL_0.6-0
>  DBI_0.2-4 RColorBrewer_1.0-2 simpleaffy_2.14.05
>  gcrma_2.10.0 matchprobes_1.10.0 genefilter_1.16.0
>  survival_2.34 affy_1.16.0 preprocessCore_1.0.0
>  affyio_1.6.1 Biobase_1.16.3
> loaded via a namespace (and not attached):
>  annotate_1.16.1 AnnotationDbi_1.0.6 rcompgen_0.1-17
>  RSQLite_0.6-8
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor