Hi, We've looked into the problem - it arises because the raw annotation data used to build the annotation files in the "hgu133a" package ommited some probesets in the latest build. This was breaking the annotation lookup calls in simpleaffy. (The issue was occuring within the results.summary() function).I've added a work around to the package to deal with this (to the devel and release 1.6 branch) - things should propagate through the servers in the next few days. Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jack Zhu Sent: 27 June 2005 19:13 To: bioconductor at stat.math.ethz.ch Subject: [BioC] error with results.summary in simpleaffy Hi all, I used functions of pairwise.filter and results.summary from simpleaffy package to do gene filtering and summarization: results <- pairwise.comparison(eset, var1,c(group1,group2), spots = data_cel) g_inten7 <- pairwise.filter(results,min.exp=1,min.exp.no=0,min.present.no=0,presen t. by.group=F,fc=0,tt=1);#trying to keep all genes summary_filtered <- results.summary(g_inten7,"hgu133a") But, I got following error: > Getting probe level data... Computing p-values Doing PMA Calls Error: value for 'AFFX-r2-Hs18SrRNA-5_at' not found When I checked 'AFFX-r2-Hs18SrRNA-5_at' in g_inten7 I did see a value in 'AFFX-r2-Hs18SrRNA-5_at'. I'm not sure if this error is associated with hgu133a and hgu133acdf or simpleaffy package. Your help will be highly appreciated. Jack Zhu, MD, MS Lombardi Cancer center Georgetown University 3970 Reservoir Rd, NW, NRB, W405b Washington, DC 20057 Email: yz8 at georgetwon.edu Tel: (202)-687-7451 Web: http://clarkelabs.georgetown.edu _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

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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 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 o...{{dropped}}

Hi, The missing hgu133a probe sets >[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" are all control probe sets, since the probe set IDs start with AFFX. In this case they appear to be ribosomal RNA probes, put on the chip to test whether the sample contains rRNA. I would imagine that nobody is really interested in the annotations for these probe sets. Regards, Maria.