Dear Sir/Madam,      Here I have two question.      First is  when I run  R in the computer, I found the computer appeared wrong message "Error: cannot allocate vector of size 214.5 Mb", what is its mean? Would you kind to  give me more suggestion?        Second question is: how to get the Gene Ontology of a list of genes?especially,if I have the gene names in the first column in the EXCEL how can I get the Gene Ontology in the second column in the EXCEL?   I have asked some people, but they only know how to get the Gene Ontology of single gene, but in my data I have thousands of genes.  Would you kind to  tell me the R commands to get the Gene Ontology file of a list of genes?    I am looking forward to hearing from you, and please send your reply to me or please tell me where can I find your reply.    Thank you very much.    Cheers   Wei __________________________________________________ [[alternative HTML version deleted]]

I am no expert, but it sounds to me as though your computer may lack sufficient memory to run the R application without quitting other applications. Look here: http://www.geneontology.org/GO.tools.microarray.shtml and here: http://www.bioconductor.org/ for some helpful info on solving your problem. Take care, Tom On Oct 29, 2009, at 8:45 PM, Sun Wei wrote: > Dear Sir/Madam, > Here I have two question. > First is when I run R in the computer, I found the computer > appeared wrong message "Error: cannot allocate vector of size 214.5 > Mb", what is its mean? Would you kind to give me more suggestion? > Second question is: how to get the Gene Ontology of a list of > genes?especially,if I have the gene names in the first column in the > EXCEL how can I get the Gene Ontology in the second column in the > EXCEL? I have asked some people, but they only know how to get the > Gene Ontology of single gene, but in my data I have thousands of > genes. Would you kind to tell me the R commands to get the Gene > Ontology file of a list of genes? > > I am looking forward to hearing from you, and please send your > reply to me or please tell me where can I find your reply. > Thank you very much. > Cheers > Wei > > __________________________________________________ > > > > [[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

We all feel that our questions are urgent. Please use a subject line that is informative about the question you are asking. And save words like "urgent" for items that affect the entire Bioconductor community and are serious, such as the Bioconductor web page sending out virulent viruses. Thanks, Naomi At 08:45 PM 10/29/2009, Sun Wei wrote: >Dear Sir/Madam, > Here I have two question. > First is when I run R in the computer, I found the computer > appeared wrong message "Error: cannot allocate vector of size 214.5 > Mb", what is its mean? Would you kind to give me more suggestion? > Second question is: how to get the Gene Ontology of a list > of genes?especially,if I have the gene names in the first column in > the EXCEL how can I get the Gene Ontology in the second column in > the EXCEL? I have asked some people, but they only know how to > get the Gene Ontology of single gene, but in my data I have > thousands of genes. Would you kind to tell me the R commands to > get the Gene Ontology file of a list of genes? > > I am looking forward to hearing from you, and please send your > reply to me or please tell me where can I find your reply. > Thank you very much. > Cheers > Wei > >__________________________________________________ > > > > [[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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Dear Wei: The message indicates some problem with memory. You need a machine with more memory. You might also try with smaller data (e.g., fewer microarrays, etc.) and see if the problem persists. There are functions that get the Gene Ontology annotation for genes in the org.xx.eg.db packages, where xx refers to the short form of the species names (Mm for Mus musculus, Hs for Homo sapiens, etc). Once you load the library, you could use the function org.Mm.egGO to map between Entrez Gene IDs and Gene Ontology. If you provide a reproducible example, it would be easier for others to understand your situation and send more helpful comments. Best wishes, Saroj Sun Wei wrote: > Dear Sir/Madam, > Here I have two question. > First is when I run R in the computer, I found the computer appeared wrong message "Error: cannot allocate vector of size 214.5 Mb", what is its mean? Would you kind to give me more suggestion? > Second question is: how to get the Gene Ontology of a list of genes?especially,if I have the gene names in the first column in the EXCEL how can I get the Gene Ontology in the second column in the EXCEL? I have asked some people, but they only know how to get the Gene Ontology of single gene, but in my data I have thousands of genes. Would you kind to tell me the R commands to get the Gene Ontology file of a list of genes? > > I am looking forward to hearing from you, and please send your reply to me or please tell me where can I find your reply. > Thank you very much. > Cheers > Wei > > __________________________________________________ > > > > [[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