Hi Ludo, James, and others, There are two separate issues. The first issue is that in some of the older tiling array library files (bpmap files) the mismatch probe was incorrectly assigned. For example, the same PM probe sequence may be present in two locations on the array and each PM probe is associated in the bpmap file with the same MM probe (rather than the physically adjacent MM probe). This is a bug and is being fixed. Contact support at affymetrix.com if you encounter such an issue and need new bpmap files. The second issue is that the same physical probe (or PM/MM probe pair for tiling arrays with MM probes) may be present in the bpmap file more than once with different genome locations. This is expected as these probes are not unique in the genome. For example in the newer Drosophila tiling array such entries exist and are valid. Best, Alan On Wed, Aug 27, 2008 at 1:08 PM, James W. MacDonald <jmacdon at="" med.umich.edu="" <https:="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > wrote: > Hi Ludo, > > Ludo Muller wrote: >> >> James, you are right about the erroneous bpmap files. I contacted >> Affymetrix about this problem and after looking into it, they confirmed >> that a lot of the mm probes have the same coordinates as the pm probes in >> the bpmap files. They are supposedly working to fix the problem, but >> couldn't give me an estimate of when they would have a corrected bpmap >> file. Thanks for reporting back. > > Interesting. I didn't look into the problem any further than to see that at > least one MM probe shares the same (x, y) coordinates (in the cdf) with > another MM probe. Although by definition the PM probes would also be > identical, in this case they have their own coordinates. > > So there are two really good (IMO) possibilities here. First, Affy just > blundered here, and the bpmap files are wrong. Apparently whomever you > talked to at Affy thinks this is the case. > > Second, since there are supposed to be probes with on average 10 bases in > between, I would have to imagine that there are a lot of probes that would > be identical. I don't know if they just blithely tile down probes regardless > of the fact that there are many replicated probes, or if they just put one > down for each replicate and then point to that one probe for the duplicates > in the bpmap file, or if they don't use the probes that aren't unique. It > has been argued in offline communications that some permutation of the above > is the case, and that we just need to change the code in pdInfoBuilder to > account for that. > > It has also been recommended that we contact a higher-up at Affy to get > confirmation which I haven't yet done, but will do now. I would suggest that you use the 'Affymetrix Scientific Community Forums': https://www.affymetrix.com/community/forums/index.jspa <https: www.affymetrix.com="" community="" forums="" index.jspa=""> for this. I quite sure that it will then be read by the "right" persons. Posting there will also "document" the issue and is much easier to refer to and follow up on later. When I've found mistakes in the NetAffx annotation files, I've been told to report to the 'NetAffx SDK' forum, so I suggest you use that too. Cheers Henrik Alan Williams | Sr. Director, Informatics | Informatics alan_williams at affymetrix.com ------------------------------------------------------------ This transmission is intended for the sole use of the individual and entity to whom it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. You are hereby notified that any use, dissemination, distribution or duplication of this transmission by someone other than the intended addressee or its designated agent is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by reply to this transmission and delete it from your computer.