[BioC] "A" mean in lmFit function in limma?

[Simon Melov]

Im trying to find the average A values for replicate chips after using 
the lmFit function. I can easily identify the average M values for each 
group of replicates, but I dont see a similar listing for the A values. 
I only appear to be generating one average A value for all replicates. 
Does the lmFit function do this, or am I doing something wrong...

thanks

Simon.


 > design <- designMatrix(targets, ref="Normal Pool")
Found unique target names:
  AD 4 Normal Pool AD 21 AD 28 AD 34 AD 35 AD 45 AD 63 AD 65 AD 66 AD 70 
AD 107
 > fit <- lmFit(MA, design)
 > fit
An object of class "MArrayLM"
$coefficients #the M average of the technical replicates for each 
sample#
             AD 4       AD 21       AD 28        AD 34       AD 35       
AD 45
[1,] -0.29077587 -0.33120458  0.05493782  0.002216203 -0.02790125 
-0.23071666
[2,]  0.03370502  0.06603841 -0.11291981  0.151881419 -0.20978938  
0.06414161
[3,]  0.17063392 -0.10746990 -0.17197063  0.011231556 -0.15972561 
-0.08339154
[4,] -0.34079507 -0.02360503  0.20886973 -0.283838031 -0.34157942  
0.13088139
[5,] -0.20889418 -0.08203535 -0.19620931  0.290167793 -0.45876852  
0.04305072
            AD 63        AD 65       AD 66        AD 70       AD 107
[1,]  0.29659220  0.029823487  0.15005839 -0.529235510  0.089936386
[2,] -0.11305790 -0.262700172  0.11602458  0.154556727 -0.006538595
[3,]  0.04773510 -0.125797143  0.10295488  0.219021314  0.098044781
[4,] -0.09582606 -0.005583817 -0.10466737  0.002683542  0.077066385
[5,] -0.01504539 -0.025666728 -0.06597346  0.234770549 -0.089887749
25083 more rows ...

$Amean #why isnt the format the same as for M?, there only appears to 
be one set of A values#
[1] 10.967244 15.627646 15.384239  7.634115 12.521264
25083 more elements ...

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