Dear Crispin,

Thanks for the effort! Though my guess was that the underlying problem 
was more due to some missing probe set annotations in the latest 
'hgu133a' package, which could in turn affect behaviour of a lot more 
packages than just 'simpleaffy'. Think about 'GOstats', just to mention 
one... :-o
But at this point, we should really change the heading of this thread! 
;-)

Best,
Norman

Norman Pavelka
Department of Biotechnology and Bioscience
University of Milano-Bicocca
Piazza della Scienza, 2
20126 Milan, Italy

Phone: +39 02 6448 3556
Fax: +39 02 6448 3552

On 11 Jul 2005, at 12:35, Crispin Miller wrote:

> Hi,
> I've added a couple of patches to simpleaffy to handle this issue with
> the annotation functions in simpleaffy. Hopefully, they'll be bubbling
> through the system at the moment.
>
> Cheers,
> Crispin
>
>
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Norman
> Pavelka
> Sent: 08 July 2005 19:27
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] error with results.summary in simpleaffy
>
> Hi all,
>
> I was about to report a similar error I encountered after my recent
> upgrade to the new 'hgu133a' package (version 1.8.4), when I saw this
> thread.
>
> My experience: After some unexplainable error messages, that were
> basically telling me that some of the probe set IDs I had found in my
> analysis had no match in the 'hgu133aACCNUM' environment, I checked the
> content of the package by typing:
>
> hgu133a()
>
> And got as answer:
>
> Quality control information for  hgu133a Date built: Created: Tue May 
> 17
> 13:02:12 2005
>
> Number of probes: 22277
> Probe number missmatch: None
> Probe missmatch: None
> Mappings found for probe based rda files:
>           hgu133aACCNUM found 22277 of 22277
>           hgu133aCHRLOC found 20195 of 22277
>           hgu133aCHR found 21283 of 22277 ......
>
> In this way I was able to immediately recognize a wrong number of probe
> sets, as 22283 were expected to be represented on this Affy chip. So I
> looked for the probe set IDs that were missing (using the 'geneNames'
> of an 'eset' containing unfiltered data from an HG-U133A experiment) by
> typing:
>
> setdiff(geneNames(eset),ls(hgu133aACCNUM))
>
> and got:
>
> [1] "AFFX-r2-Hs18SrRNA-3_s_at" "AFFX-r2-Hs18SrRNA-5_at"
> [3] "AFFX-r2-Hs18SrRNA-M_x_at" "AFFX-r2-Hs28SrRNA-3_at"
> [5] "AFFX-r2-Hs28SrRNA-5_at"   "AFFX-r2-Hs28SrRNA-M_at"
>
> So, the probe set ID 'AFFX-r2-Hs18SrRNA-5_at' (mentioned in the initial
> mail by Jack Zhu) came out again, explaining the error message he got.
> Hope this can help the great job done by the BioC developers to track
> down the possible reasons for these missing probe set IDs from the
> latest 'hgu133a' annotation package. Just to know, I was wondering when
> the fixed version was scheduled to be released...
>
> Best wishes,
> Norman
> <SNIP>
>
> --------------------------------------------------------
>
>
> This email is confidential and intended solely for the use...{{dropped}}

