Hi Dear Jim, I did it, both return a vector of name of the genes with different length,as I said before I have list of coding and noncoding so the length are not same. where is number?!
and at the end of print there is this error : <0 rows> (or 0-length row.names) On Tuesday, January 31, 2017 3:07 AM, Jim Lemon <drjimle...@gmail.com> wrote: Hi Elham, What I meant is to simply copy these two expressions into the R command line: coding.rpkm[grep("23.C",coding.rpkm$name),-1] ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1] and see what comes out. If both return a vector of numbers of the same length with no NA values, my guess was wrong. If there are NA values, try adding the argument use=pairwise.complete.obs to the "cor" statement. Jim On Tue, Jan 31, 2017 at 9:17 AM, Elham - <ed_isfah...@yahoo.com> wrote: > this script automatically recognizes what is control among cod and lnc. Note > that this script contains a piece of text that is "grep(".C",cod$name)". > This text select - among all column names - those that contain ".C". in my > files, I named C1, C2, C3, etc all columns that correspond to controls. In > the same manner, I get controls among the lnc, with the text: > "grep(".C",lnc$name)" > > I`m so sorry,maybe I do not understand you again. > > > On Tuesday, January 31, 2017 1:27 AM, Jim Lemon <drjimle...@gmail.com> > wrote: > > > Hi Elham, > This is about the same as your first message. What I meant was, what > do these two expressions return? Is whatever is returned suitable > input for the "cor" function? > > coding.rpkm[grep("23.C",coding.rpkm$name),-1] > > ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1] > > Jim > > > On Tue, Jan 31, 2017 at 8:45 AM, Elham - <ed_isfah...@yahoo.com> wrote: >> I have 9 experiments control/treatment that I analysed coding and >> lncoding, >> after that I normalize expression value.as you know we have different >> known >> number of coding and non -coding genes,so for calculating correlation >> first >> I transposed data ,(rows become columns)so row is control&treatment and >> columns are gene names.(so I have 2 matrix with same row and different >> column).This information is enough? >> >> >> >> >> On Tuesday, January 31, 2017 1:06 AM, Jim Lemon <drjimle...@gmail.com> >> wrote: >> >> >> Hi Elham, >> Without knowing much about what coding.rpkm and ncoding.rkpm look >> like, it is difficult to say. Have you tried to subset these matrices >> as you do in the "cor" function and see what is returned? >> >> Jim >> >> On Tue, Jan 31, 2017 at 6:40 AM, Elham - via R-help >> <r-help@r-project.org> wrote: >>> for calculating correlation between coding and noncoding,first I >>> transposed data ,(rows become columns) so row is control&treatment and >>> columns are gene names.(so I have 2 matrix with same row and different >>> column),I use these function for calculating correlation but all of >>> spearman >>> correlation are NA,why? >>> >>> >>> >>> >>> control.corr=cor(coding.rpkm[grep("23.C",coding.rpkm$name),-1],ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1],method= >>> "spearman") >>> >>> >>> >>> >>> >>> >>> >>> tumor.corr=cor(coding.rpkm [grep("27.T", coding.rpkm $name),-1], >>> ncoding.rpkm [grep("27.T", ncoding.rpkm $name),-1],method = "spearman") >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> 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. >> >> > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.