Begin forwarded message: > From: Rahul Kakkar <rkakkar@uchicago.edu> > Date: October 25, 2004 8:24:34 AM CDT > To: Robert Gentleman <rgentlem@jimmy.harvard.edu> > Subject: Re: [BioC] ttest genefilter 1.4.5 error on Rv2.0.0 > > Sir, > Yes. It was an error with eset$covariate. Thank you kindly for your > assistance. > -Rahul > > > On Oct 25, 2004, at 8:13 AM, Robert Gentleman wrote: > >> Did any of my suggestions work? >> >> On Thu, Oct 21, 2004 at 04:22:01PM -0500, Rahul Kakkar wrote: >>> Ran into an error running genefilter 1.4.5 on Rv2.0.0 (windows XP). >>> After updating to Rv2.0.0, Bioconductor was updated with getBioC >>> (develOK=TRUE) without issue. Genefilter was updated manually with >>> recently posted win32 build 1.4.5. >>> >>> error is the following: >>> >>>> tf1<-ttest(eset$mutant, p=.001) >>>> ff2<-filterfun(tf1) >>>> wh2<-genefilter(exprs(eset), ff2) >>> Error in model.frame(formula, rownames, variables, varnames, extras, >>> extranames, : >>> invalid variable type >>> In addition: Warning message: >>> is.na() applied to non-(list or vector) in: is.na(m) >>>> >>> >>> note input is eset generated from standard .cel file read-in: >>> >>>> data >>> AffyBatch object >>> size of arrays=1164x1164 features (42346 kb) >>> cdf=HG-U133_Plus_2 (54675 affyids) >>> number of samples=4 >>> number of genes=54675 >>> annotation=hgu133plus2 >>> >>>> eset<-rma(data) >>> >>> Attaching package 'hgu133plus2cdf': >>> >>> >>> The following object(s) are masked from package:hgu133a2cdf >>> : >>> >>> i2xy xy2i >>> >>> Background correcting >>> Normalizing >>> Calculating Expression >>> >>>> eset >>> Expression Set (exprSet) with >>> 54675 genes >>> 4 samples >>> phenoData object with 2 variables and 4 cases >>> varLabels >>> Covar1: mutant >>> Covar2: wt >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> -- >> +--------------------------------------------------------------------- >> ------+ >> | Robert Gentleman phone : (617) 632-5250 >> | >> | Associate Professor fax: (617) 632-2444 >> | >> | Department of Biostatistics office: M1B20 >> | >> | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu >> | >> +--------------------------------------------------------------------- >> ------+ >> >