Dear all, I am trying to run vsn from Limma (R version 2.6.0 (2007-10-03)) Here is my code and the return: > essai2=normalizeBetweenArrays(essai,method="vsn") vsn: 2007 x 24 matrix (1 stratum). 100% done. Warning messages: 1: The function 'vsn' is deprecated, could you please use 'vsn2' instead. 2: The exprSet class is deprecated, use ExpressionSet instead 3: The exprSet class is deprecated, use ExpressionSet instead 4: The exprSet class is deprecated, use ExpressionSet instead 5: The exprSet class is deprecated, use ExpressionSet instead 6: The exprSet class is deprecated, use ExpressionSet instead What is wrong ??? Many thnks for your help catherine

HI Catherine, nothing is wrong. The result should be alright. These mere warnings have to do with that of normalizeBetweenArrays interfacing the older (soon defunct) interface in package "vsn" and used the now outdated "exprSet" class. I believe this issue has recently been addressed by Gordon Smyth and the current development version of limma (and, of course, the version in the upcoming Bioconductor release) should not yield these warnings any longer. To clarify such potential version issues, it is advised to provide the output of sessionInfo(), when sending questions to the list. Best regards, Joern Catherine Juste wrote: > Dear all, > > I am trying to run vsn from Limma (R version 2.6.0 (2007-10-03)) > Here is my code and the return: > > essai2=normalizeBetweenArrays(essai,method="vsn") > vsn: 2007 x 24 matrix (1 stratum). 100% done. > Warning messages: > 1: The function 'vsn' is deprecated, could you please use 'vsn2' instead. > 2: The exprSet class is deprecated, use ExpressionSet instead > 3: The exprSet class is deprecated, use ExpressionSet instead > 4: The exprSet class is deprecated, use ExpressionSet instead > 5: The exprSet class is deprecated, use ExpressionSet instead > 6: The exprSet class is deprecated, use ExpressionSet instead > > What is wrong ??? > > Many thnks for your help > > catherine >