An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080303/ 53be3698/attachment.pl

Hi Jun, Jun Yin wrote: > Hi, > > My research subject focus on investigating zebrafish development using > Affymetrix GeneChip. > > I plan to reannotate the Affy Zebrafish Genechip, thus I will create a > new cdf file. As indicated in the gcrma package, I need a probe sequence > package along with the cdf file. How can I make such probe package? > > Is there any package in Bioconductor which can help to create a user-customed cdf file and probe file? The altcdfenvs package can be used to make a custom cdf. If you then want a corresponding probe package, you will need to modify the tab-delimited probe file that you can get from the Affy website to correspond to the custom cdf, and then use the matchprobes package to make the probe package. But I am a bit confused by your terminology. Re-annotating the zebrafish chip shouldn't require a different cdf and probe package. My interpretation of the term 'annotate' is the mapping of probesets to genes (or transcripts). For that task you want the AnnBuilder package. If you really are after re-mapped cdfs, you might also consider the MBNI packages. These packages use the current genome build to map probesets to genes or transcripts (based on Entrez Gene, UniGene, RefSeq, etc), which might be what you are after. There are also matching probe packages for each mapping variant, so all you would need to do is install the packages and go. For more information, please see: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/gen omic_curated_CDF.asp Also note that these are all hosted by BioC as well, so you can install using the canonical installation: source("http://www.bioconductor.org/biocLite.R") biocLite(c("drzebrafishdrentrezgcdf","drzebrafishdrentrezgprobe")) which will get you the Entrez Gene based cdf and probe packages. Best, Jim > > > > > Jun Yin > Ph.D. candidate in U.C.D. > 2008-03-03 > > Bioinformatics Laboratory > Conway Institute > University College Dublin > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080307/ 758c091c/attachment.pl