[BioC] Oligo package

Thibault Helleputte thibault.helleputte at uclouvain.be
Mon Oct 5 15:50:02 CEST 2009


I use R version 2.9.2 under MacOSX Tiger, and the oligo (1.8.3),
oligoclasses (1.6.0) and pd.hugene.1.0.st.v1 (2.4.1) packages. I
imported 20 human gene 1.0 st CEL files into R, and I summarized them
with rma(). I have then several concerns:

Once the CEL files read, I have an oligo object with 1,102,500 features,
and not 764,885 distinct probes mentioned in Affymetrix documentation.
Once this R object summarized via the rma() function, I get 253,002
features, instead of the 28,869 genes mentioned by Affymetrix. That
suggests that only 4 probes on average are included in each probesets
(roughly a 4:1 ratio between probes and summarized probesets). The
median number of probes by probesets is supposed to be 26 with that
specific technology.

Does someone have an explanation or a comment on this issue?

Many thanks.

More information about the Bioconductor mailing list