Hi, Yes I've read the vignette, and proceeded with entrez ids but I have troubles with sorting them by pvalue so the plot is messy not showing what I want. Since I've already obtained some GO ids with goseq, I could use these instead of entrez ids e.g. MF <- basicProfile (MyGoIDs[1:100], onto="MF", level=2, orgPackage="SOME.db") thus decided to ask On Wed, Oct 10, 2012 at 5:27 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > On Wed, Oct 10, 2012 at 11:21 AM, Michael [guest] > <guest@bioconductor.org> wrote: > > > > Hi, > > > > I'm trying to make nice comparison of GO profiles for three samples. > > How can do this with goProfiles, I already have GO terms and I can > easily do the profiles using entrez ids doesn't work with GO. > > I would appreciate for help. > > Did you read the vignette? > > > http://bioconductor.org/packages/2.11/bioc/vignettes/goProfiles/inst /doc/goProfiles.pdf > > It seems to show you how to do that ... you'll have to tell us what > you've tried, and why the examples in the vignette don't work for you > if you want some help. Without that, we have no idea where to even > begin to try to help. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > [[alternative HTML version deleted]]