[BioC] ttest genefilter 1.4.5 error on Rv2.0.0

Rahul Kakkar rkakkar at uchicago.edu
Thu Oct 21 23:22:01 CEST 2004

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

 > eset<-rma(data)

Attaching package 'hgu133plus2cdf':

         The following object(s) are masked from package:hgu133a2cdf :

          i2xy xy2i

Background correcting
Calculating Expression

 > eset
Expression Set (exprSet) with
         54675 genes
         4 samples
                  phenoData object with 2 variables and 4 cases
                 Covar1: mutant
                 Covar2: wt

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