hi,

i was going to normalize my microarray datasets by vsn package but i got this error

what does this mean please?

 a <- vsn(mycounts)
Note: 
The function 'vsn' has been superseded by 'vsn2'.
The function 'vsn' remains in the package for backward compatibility,
but for new projects, please use 'vsn2'.
 
Error in getIntensityMatrix(intensities, verbose) : 
  'intensities' was found to be a data.frame, but contains non-numeric columns.
> a <- vsn2(mycounts)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘vsn2’ for signature ‘"data.frame"’

You need to call vsn2 on an object that has one of the supported classes.

> showMethods("vsn2")
Function: vsn2 (package vsn)
x="AffyBatch"
x="ExpressionSet"
x="matrix"
x="NChannelSet"
x="numeric"
x="RGList"

Please have a look at the vignette of the vsn package and at the manual page of the vsn2 function, this will save you a lot of time. There is also a paper that explains the method:

Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002;18 Suppl 1:S96-104. Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M.

Wolfgang