[BioC] Rma method for library xps

cstrato cstrato at aon.at
Thu Mar 26 20:35:59 CET 2009

Dear Annamaria

If you look at the help file ?rma you will see the following:

Following exonlevel annotations are valid for whole genome arrays:
    core:     probesets with category "unique", "similar" and "mixed".
    metacore:     probesets with category "unique" only.
    affx:     standard AFFX controls.
    all:     combination of above (including affx)

Thus in your case you need to use one of:
- exonlevel = "core+affx", or:
- exonlevel = "all"

For an explanation of the different categories see the README file 
coming with the HuGene annotation, especially the section on 

Best regards
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

carissimo at tigem.it wrote:
> Dear all,
> j'm using the library xps in order to analyse some .cel file from Human
> Gene 1.0 st.
> J have the Scheme for the chip and the Root Tree for the Cel files, when J
> use the RMA method to compute expression levels, in the output file j have
> only 25927 records       instead of 33297 that is the total number of
> transcript units.
> J used this instruction
> data.rma<-
> rma(data.banfi,"DataRma",filedir=datadir,tmpdir="",background="antigenomic",
>        normalize=T,exonlevel="metacore+affx")
> Where is the problem?
> Thank you
> Annamaria Carissimo
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