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? 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@erasmusmc.nl<mailto:k.weigelt@erasmusmc.nl> [[alternative HTML version deleted]]

Hi Karin, I should also note that there won't be a cdf package for this array - Affy doesn't have one available, so you will have to use either oligo or xps (or the Affy miRNA QC tool) to process them. Best, Jim 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? > > 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=""> > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

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=""> > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099