Yes that's correct. I will give Gostats a try !! thanks. On 03/17/2011 10:43 PM, Marc Carlson wrote: > Unless you meant that you are intending to do hypergeometric testing, > (which is a different question). If that was your question, then GOstats > works well, although there are indeed many to choose from. > > Marc > > > > On 03/17/2011 02:40 PM, Marc Carlson wrote: >> Hi David, >> >> For human you want to use org.Hs.eg.db. >> >> Other packages may also contain GO terms but not mapped onto the >> correct set of genes. So if instead you had used org.Mm.eg.db, you >> would find GO terms mapped only onto mouse genes and symbols. >> >> >> Marc >> >> >> >> On 03/17/2011 02:21 PM, David martin wrote: >>> Perfect it's human, >>> I guess i can then use any of the GO packages to get signficant >>> Goterms. Which one would you suggest ? >>> >>> On 03/17/2011 10:16 PM, Marc Carlson wrote: >>>> What species? Those look like human gene symbosl, so I will give an >>>> example for that: >>>> >>>> library(org.Hs.eg.db) >>>> sym <- c("ACSL1","ADAMTSL1","ATG2B","BACH2") >>>> ## Then you can just merge together the GO to entrez gene mappings with >>>> the SYMBOL to entrez gene mappings like this: >>>> merge(toTable(org.Hs.egSYMBOL2EG[sym]), toTable(org.Hs.egGO), by.x= >>>> "gene_id", by.y="gene_id") >>>> >>>> Does that make sense? >>>> >>>> >>>> Marc >>>> >>>> >>>> On 03/17/2011 02:11 PM, David martin wrote: >>>>> Hi, >>>>> Which package should i use to convert a list of gene names >>>>> (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get >>>>> a list of significant GO terms based on the input genes).thanks for >>>>> pointing me to right direction. >>>>> >>>>> thanks, >>>>> david >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 >