Thanks Martin, I also posted the question on the bioconductor list but I have no reply yet. In the meanwhile I found out that instead of saying d=list(data.matrix2,y,censored)
I should specify the arguments: d=list(x=data.matrix2,y=y,censoring.status=censored) Strange, huh? Anyway, it solves the problem. Thanks once again, Eleni On Tue, May 6, 2008 at 6:43 PM, Martin Morgan <[EMAIL PROTECTED]> wrote: > Hi Eleni -- > > Although samr is not a Bioconductor package, you might have more luck > asking on the Bioconductor mailing list, http://bioconductor.org. The > obvious place to start, and probably you have already done this, is to > ensure that the class of the objects passed to the function agree with > the classes described on the function help page. > > Martin > > "Eleni Christodoulou" <[EMAIL PROTECTED]> writes: > > > Dear list, > > > > I am trying to perform a significance analysis of a microarray > experiment > > with survival data using the {samr} package. I have a matrix containing > my > > data which has 17816 rows corresponding to genes, and 286 columns > > corresponding to samples. The name of this matrix is data.matrix2. Some > of > > the first values of this matrix are: > > data.matrix2[1:3,1:5] > > GSM36777 GSM36778 GSM36779 GSM36780 GSM36781 > > [1,] 1.009274 1.0740659 1.048540 1.015946 1.022650 > > [2,] 1.007992 0.8768410 0.962442 1.111742 1.121150 > > [3,] 0.981853 0.9606492 1.024987 1.053302 1.063408 > > > > I also have the time in which each patient-sample is examined for > relapse. > > This information is in vector y, which has length 286, and is declared > in > > months. Indicatively: > > y[1:5] > > [1] 101 118 9 106 37 > > > > Finally, I have a variable censored, which is 1 if the patient has > relapsed > > when examined at the examined time and 0 if not. Indicatively: > > censored[1:5] > > [1] 0 0 1 0 1 > > > > > > I am trying to perform the following sam analysis: > > d=list(data.matrix2,y,censored) > > samr.obj=samr(d,resp.type="Survival", nperms=20) > > > > When I am running the above commands I get the error: > > Error in check.format(y, resp.type = resp.type, censoring.status = > > censoring.status) : > > Error in input response data: response type Survival specified; > error in > > censoring indicator > > In addition: Warning message: > > In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > > > > > > I really cannot understand what is wrong with my code. Could anyone > please > > help me with this? > > > > Thank you all, > > Eleni > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > 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. > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 > [[alternative HTML version deleted]] ______________________________________________ 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.
