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

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