Hi all, Several months ago I built a custom annotation package for Affy's Yeast 2.0 chip. Both I and the function I used gave some inconvenient names to the environments within the package and I've had some problems with annaffy because of it. My problem: An environment named "YEAST2GENENAMES" contains information normally found by annaffy under the "SYMBOL" label. An environment named "YEAST2DESCRIPTION" contains information normally found by annaffy under the "GENENAMES" label. The result of this is that nothing from DESCRIPTION is displayed (to my knowledge, annaffy doesn't handle DESCRIPTIONs), and the information in GENENAMES is displayed in the wrong place. Where do I need to do the renaming and can I do it with the package already built? Thanks in advance, Jake

On 10 Jun 2005, jzhang at jimmy.harvard.edu wrote: >> Where do I need to do the renaming and can I do it with the package >> already built? > > The environments are all in the data subdirectory of the built > package. Go there and rename the ones you like to. The environments will only be visible as .rda files if lazyLoad=FALSE was used when the data package was created. With lazyLoad=TRUE (the default), the individual rda files are "precompiled" in a lazy-loading database. Jim's suggestion to modify the accessor functions will work in either case. Another option would be to rename the environments from your R session. It might be enough to just make a copy of the environments with the right names in the global environment: NEWNAME <- OLDNAME + seth

>An environment named "YEAST2GENENAMES" contains information normally >found by annaffy under the "SYMBOL" label. > >An environment named "YEAST2DESCRIPTION" contains information >normally found by annaffy under the "GENENAMES" label. > >The result of this is that nothing from DESCRIPTION is displayed (to >my knowledge, annaffy doesn't handle DESCRIPTIONs), and the >information in GENENAMES is displayed in the wrong place. Yeast data packages were built using data source provided by SGD and thus follows SGD's's naming. If you do not like the names you may change them. > >Where do I need to do the renaming and can I do it with the package >already built? The environments are all in the data subdirectory of the built package. Go there and rename the ones you like to. > >Thanks in advance, > >Jake > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Jacob Michaelson wrote: > Hi all, > > Several months ago I built a custom annotation package for Affy's Yeast > 2.0 chip. Both I and the function I used gave some inconvenient names > to the environments within the package and I've had some problems with > annaffy because of it. > > My problem: > > An environment named "YEAST2GENENAMES" contains information normally > found by annaffy under the "SYMBOL" label. > > An environment named "YEAST2DESCRIPTION" contains information normally > found by annaffy under the "GENENAMES" label. > > The result of this is that nothing from DESCRIPTION is displayed (to my > knowledge, annaffy doesn't handle DESCRIPTIONs), and the information in > GENENAMES is displayed in the wrong place. > > Where do I need to do the renaming and can I do it with the package > already built? Look at the function aaf.handler() as well as aafSymbol() and aafDescription(). You should be able to make the necessary changes in these three functions to do what you want. You can make these changes using a built package, but the changes will be transient. Simply load the package, then source your modified functions. This will mask the existing functions for the current session. If you want more permanent changes, you will have to modify the source package and re-build. HTH, Jim > > Thanks in advance, > > Jake > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623