[BioC] XPS package working with Affymetrix GeneChip 1.0 ST at gene level

[cstrato]

Dear Jorge,

Please see the vignette "APTvsXPS.pdf" for a comparison between APT and 
xps, and see Figure 25 for the reason why xps did not implement PLIER.

I do not think that you can import the APT output into xps, at least not 
from within R (although it might be possible from C++, but I would have 
to check).

Best regards
Christian


On 6/2/12 5:20 PM, Jorge Miró wrote:
> Hi Christian,
>
> Oh, very nice. Is there any way of running PLIER in XPS too? Or is there
> any possibility of producing the expressions with Affymetrix APT and
> then use the output files in XPS to do a quality analysis within XPS?
>
> Kindly
> Jorge
>
> On Sat, Jun 2, 2012 at 5:14 PM, cstrato <cstrato at aon.at
> <mailto:cstrato at aon.at>> wrote:
>
>     Dear Jorge,
>
>     You can preprocess both, RaExon and RaGene 1.0 ST arrays, at the
>     probeset and the gene level, simply set the option to either
>     option="probeset" or to option="transcript", e.g.:
>
>     data.rma <- rma(data.genome ,"RaGeneRMAMetacore", filedir=datdir
>     background="antigenomic", normalize=TRUE, option="transcript",
>     exonlevel="metacore+affx")
>
>     See the help file ?rma.
>
>     For further examples see the scripts "script4exon.R" and
>     "script4xps.R" in the xps/examples directory. See also script
>     "script4schemes.R" how to create the scheme for the RaGene array.
>
>     Best regards
>     Christian
>     _._._._._._._._._._._._._._._.___._._
>     C.h.r.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 <http://aon.at>
>     _._._._._._._._._._._._._._._.___._._
>
>
>
>
>
>     On 6/2/12 3:02 AM, Jorge Miró [guest] wrote:
>
>
>         I was wondering if there is some way of getting the XPS package
>         working at gene level as I need to get the gene expression from
>         some Rat Gene chips (RaGene 1.0 ST r4)that I will analyze.
>
>         I tried to use the Affy package before but as far as I
>         understand they need .CDF file to get working and I only have
>         CLF and PBG files for my chips.
>
>         Kind regards
>         Jorge
>
>           -- output of sessionInfo():
>
>         -
>
>         --
>         Sent via the guest posting facility at bioconductor.org
>         <http://bioconductor.org>.
>
>         _________________________________________________
>         Bioconductor mailing list
>         Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>         https://stat.ethz.ch/mailman/__listinfo/bioconductor
>         <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>         Search the archives:
>         http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>         <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>
>