hello everyone, Just want to know if anybody has written a step by step instruction to build a affymetrix annotation package. We have some moe430_2 chips (as well as the library files) from affymetrix, but I can not find its annotation package from bioconductor meta data section. Seems the instruction of How to use Annbuilder only apply after you have data with specific format (such as two columns). But now I only have the chip library file. Regards, William

The vignette for AnnBuilder should help you get started, although it is not technically a step-by-step instruction. To get data in the specified format you can always download the annotation .csv files from the Affy website and paste the probe id and 'Sequence derived from' columns into a text editor. Alternatively, you can download the devel version of the moe430v2 package using reposTools (this may require you to use devel versions of e.g., annaffy, GO, etc.). library(reposTools) install.packages2("moe430v2", develOK=TRUE) HTH, Jim 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 >>> LIANHE SHAO <lshao2@jhmi.edu> 05/05/04 01:55PM >>> hello everyone, Just want to know if anybody has written a step by step instruction to build a affymetrix annotation package. We have some moe430_2 chips (as well as the library files) from affymetrix, but I can not find its annotation package from bioconductor meta data section. Seems the instruction of How to use Annbuilder only apply after you have data with specific format (such as two columns). But now I only have the chip library file. Regards, William _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

>Just want to know if anybody has written a step by step instruction to build a affymetrix annotation package. We have some moe430_2 chips (as well as the library files) from affymetrix, but I can not find its annotation package from bioconductor meta data section. Seems the instruction of How to use Annbuilder only apply after you have data with specific format (such as two columns). But now I only have the chip library file. I do not know what you have, but I got all the two-column mappings between AffyMetrix probe ids and GenBank, UniGene, or LocusLink ids from AffyMetrix (http://www.affymetrix.com/support). For each chip, AffyMetrix has an annotation file (e. g. Mouse430_2 Annotations, CSV (10 MB, 4/29/04)) that contains the mappings. You just need to extract the mappings you want (e. g. two column mappings between probe ids and GenBank accession numbers), make a tab (or ;, ...) separated file, and then go from there. > >Regards, >William > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084