Re: LIMMA
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Entering edit mode
@gordon-smyth
Last seen 8 hours ago
WEHI, Melbourne, Australia
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
Normalization BRAIN ASSIGN Normalization BRAIN ASSIGN • 789 views
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