[BioC] errors in FRMA

[Matthew McCall]

Mayte,

Do you mean you are trying to preprocess hgu133a2 and hgu133plus2
chips together? I wouldn't recommend this -- probe behavior (even for
identical probes) seems to differ between the 2 platforms quite a bit.

As for the hguXXXASXXFrma functions, these were replaced by
convertPlatform (for the rare cases in which one might want to
preprocess one platform as if it were really a different platform).
This is mostly for special cases like hgu133atag and hgu133a, which
differ by just a handful of probesets.

If you provide an example (with sessionInfo), I can look into why
convertPlatform might be failing.

Best,
Matt

On Sat, Apr 28, 2012 at 9:28 AM, Mayte Suarez-Farinas
<farinam at mail.rockefeller.edu> wrote:
> Hi all,
>
> I have been trying to use frma in hgu133a2 and hgu133aplus2 chips for the last 2 days unsuccessfully. I used to be able to do so with previous versions using hgu133plus2ASaFrma functions, but a call on either  functions hgu133plus2ASaFrma or hgu133a2ASaFrma produce the following result
>
> Error: could not find function "hgu133plus2ASaFrma"
>
> I tried to use then the function convertPlatform and it produces a new AffyBatch with hgu133a annotation but a call to frma(newAffyBatch)  frizzes R. When I tried to see why I discovered that the new AffyBatch has NA in the intensity slot.
>
> Thanks in advance!!
>
> Mayte Suarez-Farinas
> Research Assistant Professor,  Laboratory of Investigative Dermatology
> Biostatistician,  Center for Clinical and Translational Science
> The Rockefeller University
> 1230 York Ave, Box 178,
> New York, NY, 10065
> Phone: +1(212) 327-8213
> Fax:      +1(212) 327-8232
>
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-- 
Matthew N McCall, PhD
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