[BioC] Microarray Analysis of Rat Gene 2.0 ST arrays

[James W. MacDonald]

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
>
> --
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>
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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