Hi Tim, If your objective is to make a custom annotation package using AnnotationDbi, and a mapping that relates some probes to genes, then the SQLForge vignette in the AnnotationDbi package should tell you how to proceed. You can find some information on that here: http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.htm l If that is not what you wanted, then please let me know. Marc Tim Triche wrote: > Sort of related-ly, > > Is there a good HOWTO type of document for packaging up Illumina > annotation (CSV files/whatever) using AnnotationDbi? I don't have any > problem parsing the file formats, but the vignette provided seems a > bit Affy-centric and hard for me to adapt. I'm using R-devel and > bioconductor-2.5 for assorted reasons. > > The methylation chips in particular require a little bit of chicanery, > but that's not the problem; I'm having some issues figuring out how > and what to put into which function so that other Bioconductor > packages will know about the symbol, accession, etc. of the site being > interrogated. I wrote a bit of a hack so that 'beadarray' could > identify control probes and M vs. U probes on Infinium, but it's ugly > and it doesn't help after summarization into an ExpressionSetIllumina > or NChannelSet. I have the annotation information that I want to feed > AnnotationDbi (as well as various masks, etc.) but I'm not sure how to > structure it. > > There are a lot of (biological or sequence-related) features that can > be used for probe masking on these arrays, of course, and I have been > using several of them in an ad-hoc fashion (columns in a data frame > with IlluminaIDs as rownames, excluding rows from the exprs matrix). > I suspect there's a better way to do this, but (for example) the > 'methylumi' and 'lumi' packages don't help me in this endeavor. Is > there a customary place to store and operate upon probe masks, and is > it separate from the annotation.db packages? Is there a good role > model in terms of inheriting from a mask-able eSet class? > > Any assistance would be appreciated -- I'm sure these problems have > been addressed before, but I just couldn't figure out where. Much > obliged for anyone's time who cares to reply. > > --t > > On Fri, Sep 18, 2009 at 12:11 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> <mailto:mcarlson at="" fhcrc.org="">> wrote: > > Hi Denise, > > Unfortunately, I the answer to your question is no. The annotation > packages have had to undergo some pretty major schema changes in devel > which means that they will necessarily be incompatible with the older > version of AnnotationDbi that you will find in release. So you will > either have to use R-devel or wait a month for R-devel to become the > release version if you want to use the newer packages. In general, I > would recommend against mixing packages from different releases as > they > are not built or tested to work properly in this context. > Therefore, I > would also recommend against trying to install the newer AnnotationDbi > in the older version of R. > > For your specific case, I think you should wait a month to upgrade > your > annotation packages if you can do so. All the annotation packages are > being refreshed as we speak so that they can be current for the > upcoming > release of Bioconductor. So after the new release should be an ideal > time to upgrade. If you can't wait that long, then you can use > R-devel > with biocLite() to grab the latest packages. > > > Marc > > > > > Denise Mauldin wrote: > > Hey all, > > > > >From other posts on the list it appears that AnnotationDBI has > been updated > > for the most recent R-devel. However, I'm using the 2.5 > metadata packages > > to get the best updated information for my databases and the > hgu133a.db (and > > other affy) annotation packages require an AnnotationDBI that is > higher than > > 1.7.8. Is it possible to use these packages without upgrading > to R-devel? > > I currently have R 2.9.1 installed and I don't really want to go > to a devel > > version. Will AnnotationDBI 1.7.13 work with R 2.9.2 or is > there another > > way around this? > > > > Thanks, > > Denise > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Statisticians, like artists, have a bad habit of falling in love with > their models. > --George Box

On Fri, Sep 18, 2009 at 5:01 PM, Tim Triche <tim.triche@gmail.com> wrote: > Sort of related-ly, > > Is there a good HOWTO type of document for packaging up Illumina annotation > (CSV files/whatever) using AnnotationDbi? I don't have any problem parsing > the file formats, but the vignette provided seems a bit Affy-centric and > hard for me to adapt. I'm using R-devel and bioconductor-2.5 for assorted > reasons. > > The methylation chips in particular require a little bit of chicanery, but > that's not the problem; I'm having some issues figuring out how and what to > put into which function so that other Bioconductor packages will know about > the symbol, accession, etc. of the site being interrogated. I wrote a bit > of a hack so that 'beadarray' could identify control probes and M vs. U > probes on Infinium, but it's ugly and it doesn't help after summarization > into an ExpressionSetIllumina or NChannelSet. I have the annotation > information that I want to feed AnnotationDbi (as well as various masks, > etc.) but I'm not sure how to structure it. > > There are a lot of (biological or sequence-related) features that can be > used for probe masking on these arrays, of course, and I have been using > several of them in an ad-hoc fashion (columns in a data frame with > IlluminaIDs as rownames, excluding rows from the exprs matrix). I suspect > there's a better way to do this, but (for example) the 'methylumi' and > 'lumi' packages don't help me in this endeavor. Is there a customary place > to store and operate upon probe masks, and is it separate from the > annotation.db packages? Is there a good role model in terms of inheriting > from a mask-able eSet class? > > Any assistance would be appreciated -- I'm sure these problems have been > addressed before, but I just couldn't figure out where. Much obliged for > anyone's time who cares to reply. > Hi, Tim. You can fill the featureData slot of an ExpressionSet- derived class with a data frame of probe-specific information and seamlessly use that to subset that object. In the case of methylumi (on which I can comment directly), the featureData slot is filled with as many annotation columns as it can find in the raw data file. Is there a reason that the featureData does not meet your needs for subsetting? Sean > --t > > On Fri, Sep 18, 2009 at 12:11 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > > > Hi Denise, > > > > Unfortunately, I the answer to your question is no. The annotation > > packages have had to undergo some pretty major schema changes in devel > > which means that they will necessarily be incompatible with the older > > version of AnnotationDbi that you will find in release. So you will > > either have to use R-devel or wait a month for R-devel to become the > > release version if you want to use the newer packages. In general, I > > would recommend against mixing packages from different releases as they > > are not built or tested to work properly in this context. Therefore, I > > would also recommend against trying to install the newer AnnotationDbi > > in the older version of R. > > > > For your specific case, I think you should wait a month to upgrade your > > annotation packages if you can do so. All the annotation packages are > > being refreshed as we speak so that they can be current for the upcoming > > release of Bioconductor. So after the new release should be an ideal > > time to upgrade. If you can't wait that long, then you can use R-devel > > with biocLite() to grab the latest packages. > > > > > > Marc > > > > > > > > > > Denise Mauldin wrote: > > > Hey all, > > > > > > >From other posts on the list it appears that AnnotationDBI has been > > updated > > > for the most recent R-devel. However, I'm using the 2.5 metadata > > packages > > > to get the best updated information for my databases and the hgu133a.db > > (and > > > other affy) annotation packages require an AnnotationDBI that is higher > > than > > > 1.7.8. Is it possible to use these packages without upgrading to > > R-devel? > > > I currently have R 2.9.1 installed and I don't really want to go to a > > devel > > > version. Will AnnotationDBI 1.7.13 work with R 2.9.2 or is there > another > > > way around this? > > > > > > Thanks, > > > Denise > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > Statisticians, like artists, have a bad habit of falling in love with their > models. > --George Box > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]