Advertisement
Education

Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor

  • Michał J Okoniewski,
  • Crispin J Miller mail

    To whom correspondence should be addressed. E-mail: cmiller@picr.man.ac.uk

    X
  • Published: February 29, 2008
  • DOI: 10.1371/journal.pcbi.0040006
  • Featured in PLOS Collections

Reader Comments (2)

Post a new comment on this article

Alternative command

Posted by Julien_Textoris on 15 Apr 2012 at 09:52 GMT

x.rma <- rma(raw.data)
http://ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040006#article1.body1.sec5.sec1.sec1.p5

Hi,

with R 2.15, this command was not working for me with mouse exon array. I succeeded in loading and normalizing the data with the following lines of code. I though it may be usefull to know for someone who would experience the same problem :

phenoData = read.AnnotatedDataFrame("pheno.csv")

raw.data = ReadAffy(filenames=phenoData@data$FileName,
phenoData=phenoData,
verbose=T,cdfname="mouseexonpmcdf")

phenoData contains the same things as the covdesc file described in the article. Loadinf and PreProcessing are done in one single step (replacing lines 2, 3 and 4).

No competing interests declared.