Fwd: [BioC] ttest genefilter 1.4.5 error on Rv2.0.0

[Rahul Kakkar]

Begin forwarded message:

> From: Rahul Kakkar <rkakkar at uchicago.edu>
> Date: October 25, 2004 8:24:34 AM CDT
> To: Robert Gentleman <rgentlem at 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
>>>
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>>> 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 at jimmy.harvard.edu   
>>       |
>> +--------------------------------------------------------------------- 
>> ------+
>>
>