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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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@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@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@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 ______________________________________________ R-help@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.
