[BioC] Using vsn to normalize marrayRaw object
ZWU3 at PARTNERS.ORG
Tue Jan 10 22:04:42 CET 2006
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:
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!
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