[BioC] ttest genefilter 1.4.5 error on Rv2.0.0

[Robert Gentleman]

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
> 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
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