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Question: Missing probesets
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gravatar for Malick.PAYE@eu.biomerieux.com
13.3 years ago by
Hello all, I installed Bioconductor, the affy package as well as the makecdfenv package. I have some problems with package makecdfenv (make.cdf.package function). I'm working with a custom chip, then I tried to create a CDF package using my CDF file, when creating and installing the package everything seems to be ok but when i read my cel files I realise that about 20% of my probesets are missing. While trying to track the bug it seems that the missing probesets are those whose probes are completely/partially included in another probeset ? So I suppose that the implementation of this package prevents the inclusion of a probeset in another ? My question : what can I do to reanalyse my data with the entire probesets. I'm not familiar with C language so I can't have a look at the source code. PS : I'm using R version 2.0.1, affy version 1.5.8-1 and Makecdfenv : version: 1.4.8 If someone met this kind of problem. .. Any help would be greatly appreciate. Malick, 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]]
ADD COMMENTlink modified 13.3 years ago by rgentleman5.5k • written 13.3 years ago by Malick.PAYE@eu.biomerieux.com110
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gravatar for rgentleman
13.3 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
On May 2, 2005, at 12:16 AM, Malick.PAYE@eu.biomerieux.com wrote: > > > Hello all, > > I installed Bioconductor, the affy package as well as the makecdfenv > package. > I have some problems with package makecdfenv (make.cdf.package > function). > > I'm working with a custom chip, then I tried to create a CDF package > using > my CDF file, when creating and installing the package everything seems > to > be ok but when i read my cel files I realise that about 20% of my > probesets are missing. > > While trying to track the bug it seems that the missing probesets are > those whose probes are completely/partially included in another > probeset ? > 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 and it will not be precisely clear how to analyze such data. I suspect that some form of very large EM iteration will be 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 [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 [directions unknown] and probably should not be used - unless you have no other choices. Best wishes, Robert > So I suppose that the implementation of this package prevents the > inclusion of a probeset in another ? > > My question : what can I do to reanalyse my data with the entire > probesets. > > I'm not familiar with C language so I can't have a look at the source > code. > > PS : I'm using R version 2.0.1, affy version 1.5.8-1 and Makecdfenv : > version: 1.4.8 > > If someone met this kind of problem. .. > > Any help would be greatly appreciate. > > Malick, > > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+ +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+
ADD COMMENTlink written 13.3 years ago by rgentleman5.5k
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.
ADD REPLYlink written 13.3 years ago by Richard Finney180
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