[BioC] Rma method for library xps
cstrato at aon.at
Thu Mar 26 20:35:59 CET 2009
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
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
> Where is the problem?
> Thank you
> Annamaria Carissimo
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