[BioC] Microarray Analysis of Rat Gene 2.0 ST arrays

[Paul Geeleher]

You may also want to consider checking out Affymetrix Powertools. It
is a very straightforward piece of software and can generate output
that is easily read by R.

Paul.

On Wed, Apr 17, 2013 at 1:38 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
>
>
> On 4/16/2013 8:45 PM, Kalpana G [guest] wrote:
>>
>> I am a graduate student and new to R and Bioconductor. I have been
>> attempting to analyse microarray data from affymetrix rat gene 2.0 ST arrays
>> in R. However, I encountered problems that suggest that 2.0 arrays have not
>> been updated in Bioconductor (code and error message below).
>>
>> I wonder if I can overcome this problem by installing the appropriate
>> package? If not, please let me know if Bioconductor can currently be used to
>> analyse rat 2.0 affymetrix arrays.
>
>
> Yes, but not using the affy package. Instead you want to use either the
> oligo or xps package.
>
> Also, note that mas5 isn't really applicable for the Gene ST arrays
> (although I do believe there is some facility to emulate this in xps), as
> there are no MM probes. A more reasonable approach would be to use rma.
>
> Best,
>
> Jim
>
>
>
>>
>> Thank you.
>>
>>   -- output of sessionInfo():
>>
>>> eset.mas5=mas5(mydata)
>>
>> background correction: mas
>> PM/MM correction : mas
>> expression values: mas
>> background correcting...
>> Error in getCdfInfo(object) :
>>    Could not obtain CDF environment, problems encountered:
>> Specified environment does not contain RaGene-2_0-st
>> Library - package ragene20stcdf not installed
>> Bioconductor - ragene20stcdf not available
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
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-- 
Dr. Paul Geeleher, PhD (Bioinformatics)
Section of Hematology-Oncology
Department of Medicine
The University of Chicago
900 E. 57th St.,
KCBD, Room 7144
Chicago, IL 60637
--
www.bioinformaticstutorials.com