[BioC] error with results.summary in simpleaffy

[Ting-Yuan Liu (FHCRC)]

Hi all,

The problem of "missing probe" is the result of different 
versions of Affymetrix annotation files.  The released BioC annotation 
packages were created according to the Affymetrix annotation file which 
was released on April 1st, 2005.  There are 22277 probes included in this 
version.  The Affymetrix annotation file containing 22283 probes was 
released on June 21, 2005.  Unfortunately, you can only find the least 
version of annotation files on the website. (I happened to have the 
annotation files of April 1st, so I can figure out the answer of this 
problem.)

Affymetrix releases annotation files regularly (quarterly?) so you may 
download an annotation file from the Affymetrix website which is not 
matched with the BioC annotation packages.  Before we release new 
annotation data packages, people can try to build their own annotation 
packages based on the downloaded Affymetrix annotation files.  AnnBuilder 
is the package designed to do so.  You may find more information about 
creating annotation packages in the following vignettes:

How to use AnnBuilder
http://www.bioconductor.org/repository/devel/vignette/ABPrimer.pdf

Basic Functions of AnnBuilder
http://www.bioconductor.org/repository/devel/vignette/AnnBuilder.pdf

Of course, we will update our annotation packages as soon after 
Affymetrix release new data as possible.  

Best,
Ting-Yuan

Date: Tue, 12 Jul 2005 09:59:36 +0200
From: Norman Pavelka <norman.pavelka at unimib.it>
To: Crispin Miller <CMiller at PICR.man.ac.uk>
Cc: bioconductor at stat.math.ethz.ch
Subject: [BioC]  error with results.summary in simpleaffy

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 at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Norman
> Pavelka
> Sent: 08 July 2005 19:27
> To: bioconductor at 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}}