Re: [R] Newbie: Incorrect number of dimensions

From: Christophe Lo <christophe.lo_at_gmail.com>
Date: Sun, 02 Mar 2008 13:54:04 +0000

This is exactly what i am looking for.

many thanks
Chris

On 3/2/08, Henrique Dallazuanna <wwwhsd_at_gmail.com> wrote:
>
> You have a 'matrix' not a 'list', so
> I think you want something like this:
>
> all_differ[all_differ[, 'BY'] <= 0.01, 'BY'], this will return the
> values where column is 'BY' in all rows which is less or equal to
> 0.01.
>
>
> On 02/03/2008, Keizer_71 <christophe.lo_at_gmail.com> wrote:
> >
> > Here is the structure
> >
> > > str(all_differ)
> > num [1:6280, 1:8] 2.22e-16 2.22e-16 2.22e-16 2.22e-16 2.22e-16 ...
> > - attr(*, "dimnames")=List of 2
> > ..$ : NULL
> > ..$ : chr [1:8] "rawp" "Bonferroni" "Holm" "Hochberg" ...
> >
> > I tried, but it still giving me the same error message "Incorrect
> Dimension"
> >
> > probe.names<-all_differ[[1]][all_differ[[6280]][,"BY"]<=0.01]
> >
> > Am i using the wrong dimension?
> >
> > thanks,
> > Keizer
> >
> >
> >
> > jholtman wrote:
> > >
> > > It would be helpful if you provided commented, minimal,
> > > self-contained, reproducible code.
> > >
> > > What does str(all_differ) say? That will tell you the structure of
> > > the object that you are trying to work with.
> > >
> > > On Sat, Mar 1, 2008 at 3:35 AM, Keizer_71 <christophe.lo_at_gmail.com>
> wrote:
> > >>
> > >> > dim(data.sub)
> > >> [1] 10000 140
> > >>
> > >> #####extracting all differentially express genes##########
> > >> library(multtest)
> > >> two_side<- (1-pt(abs(data.sub),50))*2
> > >> diff<- mt.rawp2adjp(two_side)
> > >> all_differ<-diff[[1]][37211:10000,]
> > >> all_differ
> > >>
> > >> #####list of differentially expressed genes##########
> > >> > probe.names<-
> > >> + all_differ[[2]][all_differ[[1]][,"BY"]<=0.01]
> > >>
> > >> Error in all_differ[[1]][, "BY"] : incorrect number of dimensions
> > >>
> > >> Hi,
> > >>
> > >> I am pretty new with R. What i am trying to do is to find all
> > >> differentially
> > >> express genes and list of differentially expressed genes. Am i doing
> > >> something wrong?
> > >>
> > >> I keep getting incorrect number of dimensions. How do i find out the
> > >> correct
> > >> dimensions?
> > >>
> > >> thanks,
> > >> Keizer
> > >>
> > >> --
> > >> View this message in context:
> > >>
> >
> http://www.nabble.com/Newbie%3A-Incorrect-number-of-dimensions-tp15773090p15773090.html
> > >> Sent from the R help mailing list archive at Nabble.com.
> > >>
> > >> ______________________________________________
> > >> R-help_at_r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-help
> > >> PLEASE do read the posting guide
> > >> http://www.R-project.org/posting-guide.html
> > >> and provide commented, minimal, self-contained, reproducible code.
> > >>
> > >
> > >
> > >
> > > --
> > > Jim Holtman
> > > Cincinnati, OH
> > > +1 513 646 9390
> > >
> > > What is the problem you are trying to solve? Tell me what you want to
> > > do, not how you want to do it.
> > >
> > > ______________________________________________
> > > R-help_at_r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> > >
> >
> > --
> > View this message in context:
> >
> http://www.nabble.com/Newbie%3A-Incorrect-number-of-dimensions-tp15773090p15785977.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> > ______________________________________________
> > R-help_at_r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
> --
> Henrique Dallazuanna
> Curitiba-Paraná-Brasil
> 25° 25' 40" S 49° 16' 22" O
>

-- 
Christophe Lo
(078) 8275 7029
Christophe.Lo_at_gmail.com

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______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

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