I maybe being a bit obtuse but I'm trying to work out how to get an F statistic for each gene using esApply. I have factors in pData not numeric data suitable for lm e.g. fun<-function(x){ ....? } f.vector<-esApply(eset,1, fun) I can't find what I need in any of the literature. Does anyone know the command/ function I need? Thanks Stephen ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

Thanks Your reply is about half way there the rest was a problem with the model formula. It's: > fun<-function(x){lm(histo~x)$coef[1]} > f<-esApply(D.big,1,fun) in case anyone cares! Stephen -----Original Message----- From: rossini@blindglobe.net [mailto:rossini@blindglobe.net] Sent: Monday, October 06, 2003 4:17 PM To: Stephen Henderson Subject: Re: [BioC] F.test and esApply Stephen Henderson <s.henderson@ucl.ac.uk> writes: > Perhaps I am misunderstanding the way esApply works-- but trying to use lm > gives me > >> fun<-function(x){ lm(cov1~1, x)} >> f<-esApply(D.big,1,fun) > Error in eval(expr, envir, enclos) : numeric envir arg not of length one > > Which is mysterious??? No, you are returning a huge structure, not of length 1. Perhaps something like: fun<-function(x){ lm(cov1~1, data=x)$coef[1]} (untested, use str() on the results of an lm fit to find the results you are looking for -- I think you can get vectors back as well, but not sure). best, -tony > > S > > -----Original Message----- > From: rossini@blindglobe.net [mailto:rossini@blindglobe.net] > Sent: Monday, October 06, 2003 3:58 PM > To: Stephen Henderson > Subject: Re: [BioC] F.test and esApply > > > ? lm will handle factors, I think? > > best, > -tony > > Stephen Henderson <s.henderson@ucl.ac.uk> writes: > >> I maybe being a bit obtuse but I'm trying to work out how to get an F >> statistic for each gene using esApply. I have factors in pData not numeric >> data suitable for lm >> e.g. >> >> >> >> fun<-function(x){ ....? } >> >> f.vector<-esApply(eset,1, fun) >> >> >> I can't find what I need in any of the literature. Does anyone know the >> command/ function I need? >> >> Thanks >> Stephen >> >> >> ********************************************************************** >> This email and any files transmitted with it are confidentia...{{dropped}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> > > -- > rossini@u.washington.edu http://www.analytics.washington.edu/ > Biomedical and Health Informatics University of Washington > Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center > UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable > FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email > > CONFIDENTIALITY NOTICE: This e-mail message and any attachments may be > confidential and privileged. If you received this message in error, > please destroy it and notify the sender. Thank you. > > > ********************************************************************** > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they > are addressed. If you have received this email in error please notify > the system manager (wibr.mail@ucl.ac.uk). All files are scanned for viruses. > ********************************************************************** > > -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}