  Dear all,

since upgrading to the latest version of R (2.2.0) and the latest version of limma (2.4.4), backgroundCorrect(method="normexp") seems to fail. I've used this method before on a dataset of 3 dual-color chips without problems, but now, exactly the same dataset gives result like this:
   
  An object of class "RGList"
$R
               s1       s2         s3
[1,] 1.046122e+53 4.402358 2.50177231
[2,] 1.046122e+53 2.356062 4.36288331
[3,] 1.046122e+53 3.226432 3.52955031
[4,] 1.046122e+53 2.254210 4.41843931
[5,] 1.046122e+53 2.217173 0.03891324
697 more rows ...
  $G
               s1    s2           s3
[1,] 3.412653e+59 1e-06 6.411355e+49
[2,] 3.412653e+59 1e-06 6.411355e+49
[3,] 3.412653e+59 1e-06 6.411355e+49
[4,] 3.412653e+59 1e-06 6.411355e+49
[5,] 3.412653e+59 1e-06 6.411355e+49
697 more rows ...
   
   
  For reference purposes, the same data would result in the following RGlist under older versions of R and limma:
   
  An object of class "RGList"
$R
              s1       s2          s3
[1,] 3.040345497 4.389520 2.465760255
[2,] 3.419975497 2.343224 4.326871255
[3,] 4.364419497 3.213594 3.493538255
[4,] 0.003308759 2.241372 4.382427255
[5,] 4.003308497 2.204335 0.002797883
697 more rows ...
  $G
              s1        s2        s3
[1,]  9.48290819  4.130162  3.416828
[2,]  0.01069039 11.593125 12.148309
[3,] 12.21438919  3.056088  8.889050
[4,]  1.03846319 13.435718 16.352013
[5,]  6.11253719 13.028310 12.546458
697 more rows ...
   
  Could anyone advice me what is happening, and if I can do anything about it?
   
  Best regards,
   
  Bregje Wertheim
   
  Dept of Biology
  University College London
  bregjewertheim@ yahoo.com


		
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