Hi , I were certainly not enough clearly in my explanations. If I reformulate my question : what occurs when I try to create a library associated to a cdf containing probesets which are identical (the same probes have been designed for two different "targets" ( obviously these probes are not duplicated on the chip) ? Is it possible to generate expression values for all probesets from "affy" (even if there is probesets that are identical) ? Best regards, Malick, Richard Finney <rfinney5@yahoo.com> 12/05/2005 21:54 Pour : Robert Gentleman <rgentlem@fhcrc.org>, Malick.PAYE@eu.biomerieux.com cc : bioconductor@stat.math.ethz.ch Objet : Re: [BioC] Missing probesets ~ commentary from the cheap seats ... note: cutz'n'snips are from previous paye/gentleman emails ... > > be ok but when i read my cel files I realise that > about 20% of my > > probesets are missing. Which expression algorihtm are you using? MAS5 chops off high/low (i.e. two) probes for each probeset; so probesets with less than 3 probes will disappear. The 20% multigene figure for an Affy chip figure sounds about right to me. > > > > While trying to track the bug it seems that the > missing probesets are > > those whose probes are completely/partially > included in another > > Hi, > I am not sure I understand what you are saying > here. Are you saying > that some probes on your chip map to multiple > mRNA's? That does seem a > bit peculiar It's not uncommon for probes to map to multiple genes; often to members of the same gene family. Additionally there are more and more wacky run-on rnas appearing in genbank which are polluting gene to probe mappings (check out the Acembly gene track in UCSC browser for how confusing it can get). > that some form of very large EM > iteration will be Hey, what's EM ? > needed, but I would not expect anything to do it > correctly off of the > shelf. > If this supposition is correct you now need to > deal explicitly with > cross-hybridization - how much of the signal at each > such probe do you > attribute to the *different* underlying mRNA > species. This is doable, > provided there is no complete confounding - or > stated differently > provided each mRNA species has at least one probe > that is unique to it Unique? Probably not good enough. You'll still get cross hybridization from closely similar mRNAs from other genes. > [probably - there are sure to be more specific > conditions since this is > going to become a large optimization problem] - but > it is not simple to > do. > > Duplicating the probes, to give the appearance of > every gene having a > complete probe set will bias your results. Agreed. Better to mask them out or lump them into a "gene family" probeset if practical. > > > > My question : what can I do to reanalyse my data > with the entire > > probesets. > > I think Malick has a good question. You can assign probes to mulitple probesets, right? It's not that big a deal from a technical point of view. Of course, if you do, be sure to mark them as cross hybridizing and you may wish to use other technologies to verify expression of the gene in question. To repeat: masking out Multigene probes is probably a good thing. __________________________________ Yahoo! Mail Mobile Take Yahoo! Mail with you! Check email on your mobile phone. http://mobile.yahoo.com/learn/mail AVIS : Ce courrier et ses pieces jointes sont destines a leur seul destinataire et peut contenir des informations confidentielles appartenant a bioMerieux. Si vous n'etes pas destinataire, vous etes informe que toute lecture, divulgation, ou reproduction de ce message et des pieces jointe est strictement interdite. Si vous avez recu ce message par erreur merci d'en prevenir l'expediteur et de le detruire, ainsi que ses pieces jointes. NOTICE: This message and attachments are intended only for the use of their addressee and may contain confidential information belonging to bioMerieux. If you are not the intended recipient, you are hereby notified that any reading, dissemination, distribution, or copying of this message, or any attachment, is strictly prohibited. If you have received this message in error, please notify the original sender immediately and delete this message, along with any attachments. [[alternative HTML version deleted]]