You aren't providing useful details, but I have observed the problem you
mention.

Since

aafTableAnn("1000_at", "hgu133plus2.db")

works nicely, one would hope that the semantically unrelated

aafTableAnn("1000", "org.Hs.eg.db")

might do something nice too.  What happens?

> aafTableAnn("1000", "org.Hs.eg.db")
Error in get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) :
  object 'org.Hs.egORGPKG' not found

If we read some doc and thrash around a little bit we find

> aafTableAnn("1000", "org.Hs.eg.db", colnames="Symbol")
An object of class "aafTable"
Slot "probeids":
[1] "1000"

Slot "table":
$Symbol
An object of class "aafList"
[[1]]
[1] "CDH2"
attr(,"class")
[1] "aafSymbol"

So some mapping can be carried out (with translation to hyperlinked HTML by
the usual
approaches for some fields)

In fact, it seems

aafTableAnn("1000", "org.Hs.eg.db", colnames=aaf.handler()[-c(11)])

will obtain all the usual mappings except GO.  If we look at aafGO we find
that it will issue queries regarding a table named probes, but such a table
only exists in the affy annotation packages, not in org.Hs.eg.db.  It would
be nice to extend annaffy's functionality more broadly -- it works, IIRC,
with any chip-oriented product of the AnnotationDbi SQLforge (e.g., for
illumina arrays), but not with the org.* packages.

> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-05-03 r51901)
x86_64-apple-darwin10.3.0

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
 [1] hgu133plus2.db_2.4.1 org.Hs.eg.db_2.4.1   annaffy_1.21.0
 [4] KEGG.db_2.4.1        GO.db_2.4.1          RSQLite_0.8-4
 [7] DBI_0.2-5            AnnotationDbi_1.11.0 Biobase_2.9.0
[10] weaver_1.15.0        codetools_0.2-2      digest_0.4.2



On Wed, May 5, 2010 at 8:50 AM, Claudio Lottaz <
Claudio.Lottaz@klinik.uni-regensburg.de> wrote:

> Dear all,
>
> I lately used annaffy on a regular basis to generate HTML-output for  gene
> lists from Affymetrix microarray analysis. I now also need similar output
> from annotation data taken from org.Hs.eg.db and similar packages.
> Unfortunately, annaffy has difficulties to cope at least with GO and
> cytobands as far as I can see. Does anybody happen to know some workarounds
> here?
>
> Thanks for any help!
> Cheers,
> Claudio
>
>
>
> --
> ------------------------------------------------------
> Claudio Lottaz
> Computational Diagnostics, Institute for Functional Genomics
> University of Regensburg, D-93053 Regensburg (Germany)
> phone: +49 941 943 1584, fax: +49 941 5020
>
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