[BioC] removing probes from affybatch error

Wed Mar 31 19:31:34 CEST 2010

The AnnotationDbi package contains a function makeProbePackage() that 
you can use to make probe packages.

Best,

Jim

Jenny Drnevich wrote:
> 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 at gmail.com>groberts0429 at 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 at illinois.edu>drnevich at 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 at illinois.edu>drnevich at 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 at illinois.edu 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
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