[BioC] Re: LIMMA

[Gordon Smyth]

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