[BioC] problem with Oligo package when analyzing SNP6.0

[Benilton Carvalho]

Dear Ashley,

you didn't provide your sessionInfo(). It's been a while we don't use  
BufferedMatrix in oligo, so I'm guessing you need to update oligo.

For genotyping SNP 6.0 chips, this is not the recommended workflow.

A) Using oligo, you should follow the vignette:

http://www.bioconductor.org/packages/2.4/bioc/vignettes/oligo/inst/doc/oligo.pdf

ie, pretty much:

library(oligo)
filenames <- list.celfiles()
outputDir <- "someDirThatOligoWillCreateForYou"
crlmm(filenames, outputDir)

B) We have developed an enhanced version of oligo, implemented in the  
'crlmm' package, in which case you're asked to follow:

http://www.bioconductor.org/packages/2.4/bioc/vignettes/crlmm/inst/doc/genotyping.pdf

HTH,

b

On Aug 21, 2009, at 1:15 PM, Ashley Lin wrote:

> Dear all,
>
> I am trying to use oligo to analyze 75 Affy SNP6.0 chips. I have  
> installed
> BufferedMatrix, but when I do:
>
>> library(oligo)
>> filenames<-dir(pattern="CEL$")
>> rawData <- read.celfiles(filenames)
>> preProcessedData <- snprma(rawData)
>
> It gave me an error message "Error in function (classes, fdef,  
> mtable)  :
>  unable to find an inherited method for function  
> "subBufferedMatrix", for
> signature "matrix".
>
> What could be wrong?
>
> Thanks,
> Ashley Lin
>
>        [[alternative HTML version deleted]]
>
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