Hello, all,

I have some trouble with metaArray package.
I'd like use this package to integrate data from different studies. But it
give unexpected result.
I have data set with 4 time points and 2 repeats for each time. I have an
expression matrix after rma() prepossessing


> str(b.rma)
 num [1:8641, 1:8] 4.95 3.95 5.48 7.74 5.29 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:8641] "Mm.4517" "Mm.226037" "Mm.338175" "Mm.362588" ...
  ..$ : chr [1:8] "X00hr.r..CEL" "X00hr.CEL" "X08hr.r..CEL" "X08hr.CEL" ...
>  b.rma[1:5,1:4]
          X00hr.r..CEL X00hr.CEL X08hr.r..CEL X08hr.CEL
Mm.4517       4.949947  4.899200     4.814221  4.839363
Mm.226037     3.946517  4.018580     4.047994  4.000673
Mm.338175     5.484870  5.458543     5.315563  5.375122
Mm.362588     7.744338  7.761616     7.414228  7.394226
Mm.1571       5.294042  5.108926     4.720241  4.825122
>  clb <- c(1, 1, 0, 0, 0, 0, 0, 0)
> b.poe.em<- poe.em(b.rma, cl = clb,  threshold=1e-05, every = 3000)
Number of Samples: 8
Number of Genes: 8641
This model assumes that the samples are centered and scaled.
3000 genes fitted
6000 genes fitted
> b.poe.em$data[1:5,1:4]
           X00hr.r..CEL     X00hr.CEL X08hr.r..CEL    X08hr.CEL
Mm.4517    0.0639460455  0.0096282914 -0.015324771 -0.003167604
Mm.226037 -0.0221766586 -0.0003496772  0.001001762 -0.002457393
Mm.338175 -0.0005617508 -0.0057849273 -0.211710552 -0.072901889
Mm.362588  0.0153744690  0.0215050722 -0.097810670 -0.121062369
Mm.1571    0.9081874141  0.9081608456  0.015922584  0.247076490
>


I have no idea why data after poe-transformation isn't conformed with
original data.
Looking forward any suggestions!
Olga

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