Hello, How can I get ALL the Experimental Factors (Factor name, Factor values) from the Experiments on ArrayExpress? Thanks, -Yogesh [[alternative HTML version deleted]]

Yogesh Did you already have a look at the "ArrayExpress" package? Wolfgang Il Feb/4/11 12:49 AM, Yogesh ha scritto: > Hello, > > How can I get ALL the Experimental Factors (Factor name, Factor values) from > the Experiments on ArrayExpress? > > Thanks, > > -Yogesh > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber

Hi Yogesh, I do not know if there is a straightforward manner of doing this with the ArrayExpress package. You can try to modify the function queryAE from the package. Given certain keywords, queryAE outputs the following annotation: experiment ID, presence of raw/processed data in the repository, date of release, PubmedID, species, experimental design, but you can probably start from the script to output the experimental factors of all experiments without keywords. I am not sure it would work as I have never tried to do such a thing but in theory it should. You can also probably contact the ArrayExpress database people directly to ask them if there is a way to do this outside of R. Best wishes, Audrey On Fri, Feb 4, 2011 at 12:49 AM, Yogesh <yogeshp08@gmail.com> wrote: > Hello, > > How can I get ALL the Experimental Factors (Factor name, Factor values) > from > the Experiments on ArrayExpress? > > Thanks, > > -Yogesh > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Audrey, Thanks for your reply. I wanted to know if there is a straightforward way to do it. I need all the experiment factors for all the data ArrayExpress database has. This should be irrespective of the query. What you say makes sense. I will try it outside R. Just thought of asking here if the ArrayExpress package would support something like this. Thanks again, - Yogesh On Fri, Feb 4, 2011 at 6:43 AM, audrey kauffmann < akauffmann.bioinfo@gmail.com> wrote: > Hi Yogesh, > > I do not know if there is a straightforward manner of doing this with the > ArrayExpress package. You can try to modify the function queryAE from the > package. > Given certain keywords, queryAE outputs the following annotation: > experiment ID, presence of raw/processed data in the repository, date of > release, PubmedID, species, experimental design, but you can probably start > from the script to output the experimental factors of all experiments > without keywords. > > I am not sure it would work as I have never tried to do such a thing but in > theory it should. You can also probably contact the ArrayExpress database > people directly to ask them if there is a way to do this outside of R. > > Best wishes, > Audrey > > > On Fri, Feb 4, 2011 at 12:49 AM, Yogesh <yogeshp08@gmail.com> wrote: > >> Hello, >> >> How can I get ALL the Experimental Factors (Factor name, Factor values) >> from >> the Experiments on ArrayExpress? >> >> Thanks, >> >> -Yogesh >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]