[BioC] errors in FRMA

[Matthew McCall]

Mayte,

You don't need to send me a data object just your R script and your
sessionInfo. Then I can try to reproduce the error you're getting.

Matt


On Sat, Apr 28, 2012 at 3:51 PM, Mayte Suarez-Farinas
<farinam at mail.rockefeller.edu> wrote:
> 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
>



-- 
Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880