Re: Can't use package [pd.mapping250k.sty]

Hi Marcelo,

For SNP chips of that type, you want to use the oligo package, and the
crlmm function.

Best,

Jim
On Aug 8, 2014 3:23 PM, "Marcelo Pereira" <[email protected]> wrote:

> Hello,
>
> I have been trying to use the package *[pd.mapping250k.sty]*, but I’m might
> be missing something.
>
> This is my procedure:
>
> > myData <- ReadAffy()
> > myData@cdfName
>
> [1] "Mapping250K_Sty"
>
>
> The CEL fled are loaded okay!!  Then we proceed with the normalization
> procedure, and this is where the problem is:
>
> > eset <- rma(myData)
>
> *Error in getCdfInfo(object) :*
> *  Could not obtain CDF environment, problems encountered: Specified
> environment does not contain Mapping250K_Sty*
> *Library - package mapping250kstycdf not installed*
> *Bioconductor - mapping250kstycdf not available*
>
>
> Then, I tried installing it:
>
> > biocLite(‘pd.mapping250k.sty’)
> > library(‘pd.mapping250k.sty’)
>
> The package installs okay (it is a ~350Mb package), and it DOES load
> properly, but when I tried to run rma(myData) again I get the same problem
> as above:
>
> *Error in getCdfInfo(object) :*
> *  Could not obtain CDF environment, problems encountered:
> Specified environment does not contain Mapping250K_Sty*
> *Library - package mapping250kstycdf not installed*
> *Bioconductor - mapping250kstycdf not available*
>
>
> I CAN rma normalize other CEL files using hgu133plus2cdf, or hgu133acdf,
> but NOT with Mapping250K_Sty.
>
> Any suggestions?
>
> Thanks,
> Marcelo
>
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>
>
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