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

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$mutant, p=.001) > > ff2<-filterfun(tf1) > > wh2<-genefilter(exprs(eset), ff2) > Error in model.frame(formula, rownames, variables, varnames, extras, > extranames, : > invalid variable type > In addition: Warning message: > is.na() applied to non-(list or vector) in: is.na(m) > > > Some quick suggestions, questions 1) you might want to use fastT here - since it is indeed fast and all you are doing is t-tests (it is also in genefilter) 2) does this same thing happen with other data (have you tried an example data set from somewhere else?) 3) do you have a any missing values in the expression data? what is eset$mutant? just print it out, > 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 | +--------------------------------------------------------------------- ------+