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@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}}

This is surprising to me. topTable returns corrected p-value, but to my knowledge not using the q-value algorithm. Is there a new function TopTable? Not in the release version. Stefano On Tue, Jul 12, 2005 at 05:27:21PM -0400, Naomi Altman wrote: <naomi>If you are using TopTable, then you are obtaining the q-value, not the <naomi>p-value. The q-value does not have a 1-1 relationship with the t-value. <naomi> <naomi>--Naomi <naomi> <naomi>At 09:53 AM 7/12/2005, Tai, Helen wrote: <naomi>>I have been having problems with getting P values when using limma with affy <naomi>>data from the Arabidopsis AG arrays but not the ATH1 arrays. All the P <naomi>>values from the AG data are 0.999984 even though the t statistic is varying <naomi>>in value. Has anyone else had this problem? <naomi>> <naomi>>Helen <naomi>> <naomi>>_______________________________________________ <naomi>>Bioconductor mailing list <naomi>>Bioconductor at stat.math.ethz.ch <naomi>>https://stat.ethz.ch/mailman/listinfo/bioconductor <naomi> <naomi>Naomi S. Altman 814-865-3791 (voice) <naomi>Associate Professor <naomi>Bioinformatics Consulting Center <naomi>Dept. of Statistics 814-863-7114 (fax) <naomi>Penn State University 814-865-1348 (Statistics) <naomi>University Park, PA 16802-2111 <naomi> <naomi>_______________________________________________ <naomi>Bioconductor mailing list <naomi>Bioconductor at stat.math.ethz.ch <naomi>https://stat.ethz.ch/mailman/listinfo/bioconductor -- Stefano Calza, PhD Sezione di Statistica Medica e Biometria Dip. di Scienze Biomediche e Biotecnologie Universit? degli Studi di Brescia - Italia Viale Europa, 11 25123 Brescia email: calza at med.unibs.it Telefono/Phone: +390303717532 Fax: +390303717488 Section of Medical Statistics and Biometry Dept. Biomedical Sciences and Biotechnology University of Brescia - Italy