[BioC] Chip Definition File (CDF) for Affymetrix microRNA Arrays 3.0

[James W. MacDonald]

HI Karin,


On 4/26/2013 9:47 AM, K. Weigelt wrote:
> Dear Sir or Madam,
>
> I would like to analyze array data from Affymetrix microRNA microarray platform 3.0 using BRB array tools,
> but it seems that like there is no CDF file available for these arrays yet?
>
> I could find the "pd.mirna.3.0" package, but this doesn't seem to include the CDF file?

That is the corresponding file for the oligo package. So you can do 
pretty much the exact same thing using oligo that you wanted to do with 
affy:

library(oligo)
dat <- read.celfiles(list.celfiles())
eset <- rma(dat)

Best,

Jim


>
> Thank you very much for your help!
>
> Kind regards,
> Karin Weigelt
>
> Karin Weigelt, PhD
> Department of Immunology
> Erasmus Medical Center
> Dr. Molewaterplein 50
> 3015 GE Rotterdam
> The Netherlands
> Phone    : + 31 10 704 4108
> Fax    : + 31 10 704 4731
> Email: k.weigelt at erasmusmc.nl<mailto:k.weigelt at erasmusmc.nl>
>
>
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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