[BioC] Using vsn to normalize marrayRaw object

Tue Jan 10 22:04:42 CET 2006

Hi, There,

I read the vsn vignettes. Although it says that vsn can take a marrayRaw object,
there isn't any example that shows how to normalize the marrayRaw object. When I
input a marrayRaw object called west2005Raw which is an output of read.SMD, I
got the following:

> vsn(west2005Raw)
Converting marrayRaw (41088 spots, 57 slides) to 41088x114 matrix.
 Gf-Gb in odd columns, Rf-Rb in even columns.
Error in getIntensityMatrix(intensities, verbose) :
        'intensities' must not contain NA values.
 This could indicate that the input data has already undergone some
 thresholding or transformation (log?), and may not satisfy the
 requirements of the multiplicative-additive noise model.
 If you are sure that it is meaningful to proceed, please
 consider calling vsn on a subset of data where all values
 are defined, and then use vsnh on the full set of data.

It seems that vsn normalizes the Gf-Gb and Rf-Rb seperately, and it doesn't take
care of the NAs which directly come from the read.SMD result. Anyone has any
experience with this? 

I am using R 2.2.0 on Linux.

Thanks in advavnce!

Zhuang Wu

More information about the Bioconductor mailing list