[BioC] Limma: bad spots flagged out?

[Ana Conesa]

   Dear list,
   I   have   a  doubt  about  the  real  use  of  spots  weights  during
   normalization in limma. According with the documentation spots weights
   equal  to  0  are  ignored  during  normalization (and other posterior
   analyses)  , and although these spots are not removed they do not have
   any  influence on the rest. I had observed some strange behavior on my
   normalized  data  and made a tried to make a check on this. What I did
   was  to  replace  weights==0 spots by NA and redo analysis. I have
   found  the  results  do  no   spots  are  adequately ignored by limma or I made a conceptual mistake
   in this check. This is exactly the code I used for checking:
   > RG.b <- backgroundCorrect(RG)
   > MA.1 <- normalizeWithinArrays(RG.b)
   > RG.b$G[RG.b$weights==0] <- NA
   > RG.b$R[RG.b$weights==0] <- NA
   > MA.2 <- normalizeWithinArrays(RG.b)
   > MA.1$M[2,]
            BFN33        S50.05        S65.02        S65.03        S71.02
   S75.01      S77.03     control     control     control     control
   -0.96794887     0.06715693    -0.08766477    -0.50161127   -1.25216169
   -0.80724650    -0.61351625    -0.80751427    -0.49960303   -0.66912129
   0.27447918
   > MA.2$M[2,]
            BFN33        S50.05        S65.02        S65.03        S71.02
   S75.01      S77.03     control     control     control     control
   -0.94108221     0.04803980    -0.08030398    -0.49226094            NA
   -0.79588160             NA    -0.77182854             NA   -0.61426784
   0.18076174
   Thank you
   Ana

      O @@@@@     Ana Conesa, PhD.
     @@@ O @@ O @   Centro de Genómica
      @  O  @@@@  O  @   Instituto Valenciano de Investigaciones Agrarias
   (IVIA)
     @@@ O @@@@        @@@@ O @     46113 Moncada (Valencia) SPAIN
        ||       Tel. +34 963424000 ext.70161; Fax. +34 963424001
        ||       email: aconesa at ivia.es