Entering edit mode
At 09:20 PM 18/06/2003, muehleisen wrote:
>Dear Dr. Smyth,
>
>Unfortunately, I pushed the send button of my email program although
I
>hadn't written my email completely.
>
>Using "normalizeWithinArrays" it is possible to assign spot quality
>weights to each slide. If the object is a RG list, weights will be
>assigned by default. On the other hand, the "weight" argument can be
>stated explicitly.
>
>Regarding "normalizeForPrintorder" and "PlotPrintorder" does the
"weight"
>argument function equivalently?
No, as you can see from the documentation, there is no "weight"
argument.
There is no reason in principle why normalizeForPrintorder couldn't
accept
a weight function, but I haven't implemented it.
loess is quite a robust method, so that a small proportion of poor
quality
points will not cause it a problem. I would be wary of using the
GenePix
weights for printorder normalization because they are no heavily
related to
intensity.
normalizeForPrintorder is still a somewhat experimental function which
we
use only occasionally.
Best wishes
Gordon
> In my opinion it could be very useful using these functions if bad
> flagged spots are weighted down. In general, are virtually any spots
> which are negatively flagged (-100: bad, -75: absent, -50: not
found)
> assigned by a weight of 0.1?
>
>I hope that my questions don't bother you but they're very important
for me.
>
>Thank you again in advance!!!!
>
>Sincerely,
>
>Thomas W. Muehleisen
>
>Max Planck Institute for Brain Research
>Deutschordenstrasse 46
>D-60528 Frankfurt/Main