Whoops yes I see that now, I guess you first need to figure out what kind of gene ids you have. That DAVID tool I spoke of can often autodetect the type of gene id you are trying to convert if they are in its database. Paul. On Wed, Jan 12, 2011 at 11:06 AM, Budhayash Gautam <budhayashgautam at="" gmail.com=""> wrote: > Thanks Paul for reply, > > ?no these are not affy ids , i am working on two color data. > > On Wed, Jan 12, 2011 at 4:30 PM, Paul Geeleher <paulgeeleher at="" gmail.com=""> wrote: >> Are they affy ids? Maybe the gene ID conversion tool might be able to >> help: http://david.abcc.ncifcrf.gov/conversion.jsp >> >> Paul. >> >> On Wed, Jan 12, 2011 at 9:42 AM, Budhayash Gautam >> <budhayashgautam at="" gmail.com=""> wrote: >>> Hello friends, >>> >>> i am working on some SMD two color data for Toxoplasma gondii , i have >>> done differential expression analysis. Now i want to annotate these >>> genes, >>> >>> now the problem is that how can i convert the probe ID's to Gene names >>> using annotation package and with what database because there is no >>> database in bioconductor related to t. gondii. >>> >>> if i have to pick these gene names from NCBI then how can i link or >>> retrieve this information from ncbi collectively as i have to do these >>> annotation on the level of genome so no. of genes are in thousands... >>> >>> or if any one can suggest any reading material it will be helpful to >>> me becoz i am stuck right now how to go ahead..... >>> >>> -- >>> BUDHAYASH GAUTAM >>> Assistant Professor >>> Department Of Computational Biology And Bioinformatics, >>> Jacob School of Biotechnology & Bioengineering (JSBB) >>> Sam Higginbottom Institute of Agriculture, Technology and Sciences >>> (SHIATS)- Deemed University, Naini, Allahabad. >>> U.P. 211007 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> >> -- >> Paul Geeleher (PhD Student) >> School of Mathematics, Statistics and Applied Mathematics >> National University of Ireland >> Galway >> Ireland >> -- >> www.bioinformaticstutorials.com >> > > > > -- > BUDHAYASH GAUTAM > Assistant Professor > Department Of Computational Biology And Bioinformatics, > Jacob School of Biotechnology & Bioengineering (JSBB) > Sam Higginbottom Institute of Agriculture, Technology and Sciences > (SHIATS)- Deemed University, Naini, Allahabad. > U.P. 211007 > -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com