[BioC] RMA in xps does not use HuEx-1_0-st-v2.r2.antigenomic.bgp file. Possible ERROR?

[cstrato]

Dear Addiel,

The reason is that the antigenomic.bgp file contains redundant 
information which is already present in the HuEx-1_0-st-v2.r2.pgf file.

Simply search the pgf-file for: control->bgp->antigenomic

BTW, in function rma() "antigenomic" is only a parameter which is 
internally used for the mask. Function rma() still uses the PMs only for 
background correction of exon arrays. Probably I should clarify this 
issue in the help file.

If you want to use antigenomic probes for background correction you need 
to call function bgcorrect.gc().

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
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On 1/29/11 1:39 AM, Addiel de Alba wrote:
>
> Hi All,
>
> In the script4exon.R provided with the xps package. There is no indication that
> you should upload the antigenomi.bgp file. However, the function for RMA claims
> to use the antigenomic probes. How is this possible?
>
> Thank you
>
> Addiel
>
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