[BioC] how to merge replicate spots?

[Barbara Cegielska]

Michael,

No, it wasn't deliberate. I've change it and it seems  to work. Is it 
correct?

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 > fit <- lmFit(a, design)
 > contrast.matrix<-makeContrasts(AML.M2-K,levels=design)
 > fit2<-contrasts.fit(fit,contrast.matrix)
 > fit2<-eBayes(fit2)
 > topTable(fit2,adjust="BH")
    Block Row Column    ID    Name Status     logFC  AveExpr         
t      P.Value  adj.P.Val        B
850    35   6      1  6767    ST13 Oligos  3.075192 7.234434  9.388662 
7.710111e-05 0.02516929 2.306532
284    11   5      4  6280  S100A9 Oligos -3.005805 8.759735 -9.303701 
8.122192e-05 0.02516929 2.257757
859    35   9      1 23166   STAB1 Oligos  2.929309 7.131428  9.017997 
9.706814e-05 0.02516929 2.089691
841    35   3      1  6726    SRP9 Oligos  2.847275 7.485457  8.970909 
1.000094e-04 0.02516929 2.061377
557    21   6      4  3717    JAK2 Oligos  2.315902 8.071873  8.413855 
1.439105e-04 0.02516929 1.712576
854    35   7      4  4772  NFATC1 Oligos  2.453980 7.217102  8.247170 
1.611193e-04 0.02516929 1.603018
785    33   2      4  6093   ROCK1 Oligos  2.256970 7.425680  8.150150 
1.722239e-04 0.02516929 1.538097
436    17   2      1  3563   IL3RA Oligos  2.554791 7.891780  7.911541 
2.034941e-04 0.02530803 1.374718
937    37  10     10   291 SLC25A4 Oligos  2.507008 8.085160  7.737719 
2.304150e-04 0.02530803 1.252276
972    37  17     10   369    ARAF Oligos  2.282989 6.985434  7.484587 
2.772916e-04 0.02530803 1.068606
 > dim(fit2)
[1] 1023    1

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P.s Sorry for not keeping discussions "on the list".

Regards,
B.