Re: [R] Newbie: Incorrect number of dimensions

From: Henrique Dallazuanna <wwwhsd_at_gmail.com>
Date: Sun, 02 Mar 2008 08:33:35 -0300

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

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Received on Sun 02 Mar 2008 - 11:39:11 GMT

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