Hi George,

I've never made a probe package either? Did you try searching the 
BioC archives for "make probe package"?

http://dir.gmane.org/gmane.science.biology.informatics.conductor

Also, you forgot to post to the BioC list as well!

Cheers,
Jenny

At 08:40 AM 3/31/2010, George Roberts III wrote:
>Hi Jenny,
>
>I installed the .CDF package for my chips but still don't know how 
>to make a cdfprobe package and couldn't find any further info.
>
>Thanks for your help,
>George
>
>On Sat, Jan 23, 2010 at 11:58 PM, George Roberts 
><<mailto:groberts0429@gmail.com>groberts0429@gmail.com> wrote:
>Hi Jenny,
>
>Sorry for not posting in the BioC list, I will in the future; I 
>found the URL where you posted the previous email but don't know how 
>to reply to that thread so I replied to this email instead.
>
>I spoke with the designers of the custom chip to find some insight 
>into the "NA" issue. All of the "NA" values were traced to a series 
>of probes that consist of only a single PM probe for each gene. They 
>were analyzed with GCOS and none gave "NA"; all gave a number. The 
>individual who performed the first analysis had no further insight 
>into whey R might have behaved this way. I want to exclude these 
>probes from my analysis in any event.
>
>Thanks for pointing out that this error had to do with not 
>installing the .CDF package. I had loaded the .CDF environment in 
>the belief that it would be enough. Installing the .CDF package and 
>.CDFprobe package will be my next step.
>
>Thank you very much for your help,
>George
>
>
>On Tue, Jan 19, 2010 at 9:38 AM, Jenny Drnevich 
><<mailto:drnevich@illinois.edu>drnevich@illinois.edu> wrote:
>Hi George,
>
>Sorry I haven't been able to respond - I've been extremely busy. 
>It's actually better to post questions like this to the BioC list 
>instead of to one poster directly - you might get a more timely 
>response, and it's good to have the response in the archives so 
>other people can access it. Your error message is pretty simple - 
>you don't have package mpauta520274cdfprobe. I'm guessing this is a 
>custom Affy array, so in addition to the mpaut1a520274fcdf package, 
>you'll need a mpaut1a520274fprobe package to be able to use the 
>RemoveProbes function "as is" and other functions like gcrma(). I 
>forget off the top of my head what you need to do to make the probe 
>package, so perhaps others will comment. If you can't make the probe 
>package and only want to remove entire probe sets, then the code of 
>RemoveProbes might be able to be modified to work without the probe 
>package. Unfortunately, I won't have time for a couple of weeks to 
>look at it. Feel free to hack it all you want if you can!  Sorry I 
>can't be of more help right now...
>
>Jenny
>
>P.S. What's going on with your scans that you are getting "NA" 
>values for individual probes? That's very odd!
>
>
>At 05:48 PM 1/12/2010, George Roberts wrote:
>>Dr. Drnevich,
>>
>>I would like to use your code 
>><https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html>https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html 
>>to remove some probesets that are causing "NA" values resulting in 
>>errors. My CDF is "MPAUT1a520274F.CDF". I get the following error messages:
>>
>> > RemoveProbes(listOutProbes=NULL, listOutProbeSets="
>>+ 1415670_at
>>+ 1415671_at
>>+ 1415672_at
>>+ ", cleancdf)
>>Loading required package: mpaut1a520274fcdfcdf
>>Loading required package: mpaut1a520274fcdfprobe
>>Error in get(probepackagename) :
>>   object 'mpaut1a520274fcdfprobe' not found
>>In addition: Warning messages:
>>1: In library(package, lib.loc = lib.loc, character.only = TRUE, 
>>logical.return = TRUE,  :
>>   there is no package called 'mpaut1a520274fcdfcdf'
>>2: In library(package, lib.loc = lib.loc, character.only = TRUE, 
>>logical.return = TRUE,  :
>>   there is no package called 'mpaut1a520274fcdfprobe'
>>
>>Thanks,
>>George Roberts
>>Wayne State University
>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: <mailto:drnevich@illinois.edu>drnevich@illinois.edu
>
>

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@illinois.edu 
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