[BioC] errors in FRMA

[Mayte Suarez-Farinas]

Thanks Matthew,

I am trying to preprocess two batches, hgu133a2 and hgu133plus2 separately using frma but I want to
then subset for the set of common probes, that's why I want to frma hgu133plus2 chips to hgu133a anyway,
I try the convertPlatform but as I said it did not work out. DO you me to send you  affybatch ?
 Txs
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










On Apr 28, 2012, at 3:38 PM, Matthew McCall wrote:

> 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
> 112 Arvine Heights
> Rochester, NY 14611
> Cell: 202-222-5880