[BioC] Help on Loading AgilentData into LIMMA
  ----- Original Message ----- 
  From: Nataliya Yeremenko 
  To: bioconductor@stat.math.ethz.ch 
  Sent: Tuesday, November 01, 2005 5:43 PM
  Subject: [BioC] Help on Loading AgilentData into LIMMA


  I need help on loading data to LIMMA 
  I'm working with 44K Agilent microarrays. 

  I'm novice in BioConductor, so I'm trying to follow instructions on the 
  packages 
  to deal with my data. 

  I'm trying to load Feature Extraction raw data with 
   > RG <- read.maimages(files = targets$fileName, path = loadPath, source 
  = "agilent") 
  and data seems to be loaded fine, where targets is experiment 
  description file. 
  It is loading all my 20 replicates, 
  but when I checked RG data set with dim(RG) or show(RG) 
  I realized that only 6195 rows have been loaded. 
  It is the same situation independent on how many arrays I'm loading 1 or 28. 
  Is there limit for number of spots in the package? 



  I've tried to start as well with arrayMagic package 
  and again didn't succeed to load even single array, 
  After 10 min of loading I see error message stating 
  that line 17000 has not proper amount of arguments. 

Nataliya,

This is a problem with Agilent image extraction files--they have some special characters according to R that preclude their loading correctly.  I will forward a perl script that I use to "clean" such files tomorrow, but I don't think this is a problem with limma (and probably not arrayMagic).  

Sean

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