Profiles
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@guest-user-4897
Last seen 6.6 years ago
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. Best! -- output of sessionInfo(): a -- Sent via the guest posting facility at bioconductor.org.
GO goProfiles GO goProfiles • 535 views
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@steve-lianoglou-2771
Last seen 2 days ago
Denali
Hi, On Wed, Oct 10, 2012 at 11:21 AM, Michael [guest] <guest at="" 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/d oc/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
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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]]
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