Entering edit mode
At 12:10 AM 27/08/2003, michael watson (IAH-C) wrote:
>... I can't put it much simpler than the subject... if I take the
same set
>of data and loess normalise it using both packages, accepting the
>defaults, the values that come out differ by approximately +/- 0.02
each
>time....
Which versions of the packages are you using? There are several
different
loess normalization methods, which one did you use? Are you using
weights?
It would be best to give the actual commands you used in the two
packages.
>Is there a reason for that? Perhaps some rounding up or something?
No there are other differences. In the latest versions of the
packages,
marrayNorm uses span=0.4 by default while limma uses span=0.3. This
would
easily produce the difference you see. (No doubt you have already
checked
the documentation for such an obvious cause as this.) Other very small
differences arise because limma uses lowess when there aren't any
weights
and loess when there are, while marrayNorm uses loess throughout.
Gordon