Dear all I would like to use the package 'geneplotter' which requires a Bioconductor data package. I cannot see a Bioconductor data package for the Nimblegen HG18 promoter arrays, so I will need to make my own. Based on what I can see in the mailing list, I believe that I need to use AnnotationDbi, and modify the function makeProbePackage to read in NimbleGen (as opposed to Affymetrix data). Could anyone confirm that I am on the right track?/show me any useful pointers? with many thanks for your time, Lavinia Gordon. 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. http://www.mcri.edu.au/

On Wed, Aug 5, 2009 at 4:28 AM, Lavinia Gordon <lavinia.gordon@mcri.edu.au>wrote: > > Dear all > I would like to use the package 'geneplotter' which requires a > Bioconductor > data package. > I cannot see a Bioconductor data package for the Nimblegen HG18 promoter > arrays, so I will need to make my own. > Based on what I can see in the mailing list, I believe that I need to use > AnnotationDbi, and modify the function makeProbePackage to read in > NimbleGen > (as opposed to Affymetrix data). > Could anyone confirm that I am on the right track?/show me any useful > pointers? > with many thanks for your time, > There are other ways to go here. You could try the Ringo, ACME, tilingArray, or oligo packages for data import and analysis. Each also has graphical functions for output. For graphics, you could additionally look at GenomeGraphs and rtracklayer. Sean [[alternative HTML version deleted]]

Hi Sean Many thanks for your email. I have tried most of the packages that you mention and have had some very pleasing results. Specifically I am interested in using the cPlot function of geneplotter. I could not see a similar function in any other packages (genome wide as opposed to just chromosome wide display). with regards Lavinia. At 07:46 AM 5/08/2009 -0400, Sean Davis wrote: On Wed, Aug 5, 2009 at 4:28 AM, Lavinia Gordon <[1]lavinia.gordon at mcri.edu.au> wrote: ?? Dear all ?? I would like to use the package 'geneplotter' which requires a Bioconductor ?? data package. ?? I cannot see a Bioconductor data package for the Nimblegen HG18 promoter ?? arrays, so I will need to make my own. ?? Based on what I can see in the mailing list, I believe that I need to use ?? AnnotationDbi, and modify the function makeProbePackage to read in NimbleGen ?? (as opposed to Affymetrix data). ?? Could ?? anyone confirm that I am on the right track?/show me any useful ?? pointers? ?? with many thanks for your time, ?? There are other ways to go here.?? You could try the Ringo, ACME, tilingArray, or oligo packages for data import and analysis.?? Each also has graphical functions for output.?? For graphics, you could additionally look at GenomeGraphs and rtracklayer.?? Sean ?? Lavinia Gordon Research Officer Bioinformatics Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia telephone: +61 3 8341 6221 [2]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. mailto:lavinia.gordon at mcri.edu.au 2. http://www.mcri.edu.au/