Dear Martin Thank you so much for your email. I had been sidetracked by 'makeProbePackage' and was getting nowhere. The instructions in the vignette are very easy to follow, worked a treat for both of my sets of data. Many thanks, Lavinia. At 11:01 AM 26/08/2009 -0700, Martin Morgan wrote: Lavinia Gordon wrote: > Dear All, > Following on from Axels email, this is exactly what I would like to do, but > I am not using Affymetrix data. Can anyone give me some pointers on how to > create an Bioconductor data package (i.e. like hgug41112a), but for > NimbleGen data. Hi Lavinia -- you can create your own annotation packages following instructions in the 'SqlForge' vignette associated with the AnnotationDbi package, available here, for instance [1]http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html If that is not appropriate (e.g., non-model organism) then for this particular case (using cPlot) you could try to construct a 'chromLocation' object from information you've obtained from other sources (e.g., NimbleGen) about chromosome location of each probe. There are hints on what this should look like on the help page ?"chromLocation-class"; you're aiming to be able to call 'new' with appropriate arguments. Some other hints about what the data is supposed to look like might come from inspecting the object 'z' produced by the code in the cPlot example. Martin > with many thanks for your time, > Lavinia Gordon. > > Message: 6 > Date: Mon, 24 Aug 2009 19:15:29 +0200 > From: Axel.Klenk at Actelion.Com > Subject: [BioC] chromosome ordering in cPlot()/cColor() > To: bioconductor at stat.math.ethz.ch > Message-ID: > <12450_1251134133_4A92CAB5_12450_361234_1_OFDD2C6357.89EE7981-ONC1 > 25761C.005CC5F4-C125761C.005ECE81 at actelion.com> > > Content-Type: text/plain; charset=US-ASCII > Dear Biocore Team, > I'm using cPlot()/cColor() from package annotate to produce chromosome > plots and > am very impressed how easily this can be achieved. However, unfortunately, > the > chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11, > etc. > from bottom > to top and I would like to reorder them to 1, 2, 3, ... from top to bottom > but cannot find an > easy way to do so... am I missing something here? > I managed to get what I want by hacking buildChromLocation() but that's > ugly and I don't > want to maintain a modified function if not necessary. > Would it be possible to add a replace method for the chromInfo slot to > allow e.g. > z <- buildChromLocation("hgug41112a") > library("gtools") # for mixedsort() > info <- chromInfo(z) > chromInfo(z) <- info[rev(mixedsort(names(info)))] > or maybe you can think of a better solution? > Thanks in advance, > - axel > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > > Lavinia Gordon > Research Officer > Bioinformatics > Murdoch Childrens Research Institute > Royal Children's Hospital > Flemington Road Parkville Victoria 3052 Australia > telephone: +61 3 8341 6221 > [1]www.mcri.edu.au > This e-mail and any attachments to it (the "Communication") are, unless > otherwise stated, confidential, may contain copyright material and is for > the use only of the intended recipient. If you receive the Communication in > error, please notify the sender immediately by return e-mail, delete the > Communication and the return e-mail, and do not read, copy, retransmit or > otherwise deal with it. Any views expressed in the Communication are those > of the individual sender only, unless expressly stated to be those of > Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its > related entities. MCRI does not accept liability in connection with the > integrity of or errors in the Communication, computer virus, data > corruption, interference or delay arising from or in respect of the > Communication. > Please consider the environment before printing this email > > References > > 1. [2]http://www.mcri.edu.au/ > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > [3]https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: [4]http://news.gmane.org/gmane.science.biology.informatics.conductor Lavinia Gordon Research Officer Bioinformatics Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia telephone: +61 3 8341 6221 [5]www.mcri.edu.au This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. Please consider the environment before printing this email References 1. http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html 2. http://www.mcri.edu.au/ 3. https://stat.ethz.ch/mailman/listinfo/bioconductor 4. http://news.gmane.org/gmane.science.biology.informatics.conductor 5. http://www.mcri.edu.au/