Fw: [BioC] Affy Bioconductor with Rat230_2 chips

[Ali A. Pirani]

Dear Crispin (or anybody),

According to your message, the new version of simpleaffy will fix this error,
but we seem to sill be encountering it.  Is the latest version of simpleaffy
1.3.2 found on this page:

http://bioconductor.org/repository/devel/package/html/simpleaffy.html

?

Any assistance will be appreciated, because even though we updated all of our
installations, we still see the below error message.

Thanks,

Ali
BIMCORE


"Kim Gernert" <gernert at emory.edu> on Wednesday, May 05, 2004 at 2:37 PM -0500
wrote:
>
>Kim M. Gernert
>Director     BimCore
>mail:  4001 Rollins Research Ctr
>loc:   G236 Biochem. Connector
>Emory University
>Atlanta, GA  30322
>ph     404-727-3501
>fax    404-727-5512
>----- Original Message ----- 
>From: "Crispin Miller" <CMiller at PICR.man.ac.uk>
>To: "Kim Gernert" <gernert at emory.edu>
>Cc: <bioconductor at stat.math.ethz.ch>
>Sent: Monday, April 26, 2004 2:57 AM
>Subject: RE: [BioC] Affy Bioconductor with Rat230_2 chips
>
>
>> Hi Kim,
>> The new version of simpleaffy has a lot of bug fixes and stuff in it, so
>> I'd suggest using it anyway... ;-)
>>
>> The qc.stats code needs to know which chip you're using, to pick the
>> right spike probes - and detection p-value stuff needs to use it to work
>> out which alpha1 and alpha2 parameters to use...
>> I'm going to modify the code so you can specify the probes you wish to
>> use and stuff like that. In the next day or two I'll add the rat2302cdf
>> to the lists and upload a new version...
>> Cheers,
>> Crispin
>>
>>
>> -----Original Message-----
>> From: bioconductor-bounces at stat.math.ethz.ch
>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Kim Gernert
>> Sent: 23 April 2004 20:35
>> To: bioconductor at stat.math.ethz.ch
>> Subject: [BioC] Affy Bioconductor with Rat230_2 chips
>>
>>
>>
>> I am trying to process Affymetrix array data from the new rat chip
>> (RAT230_2). We followed the vignette on setting up the new rat230-2.cdf
>> file and all seemed
>> fine  (readaffy, rnadeg..., rma, etc.)  until I tried
>>
>> (simpleaffy)  qc.stats
>>
>> ERROR: I am sorry I donot know spike probes on rat230.2.cdf
>>
>>
>> Do I need the new simpleaffy (last download Mar 2004), do I need the new
>> R (currently running 1.8.1, on Linux)? or is there an additional script
>> I need to run to inform R of the new parameters
>> (spikes, etc.) for the RAT230_2?
>>
>>
>> Your help is appreciated.
>>
>> Kim M. Gernert
>>
>>
>>
>>
>> ---
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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