Hi all,

Is there anybody who is familiar with the Paired Data Analysis in baySeq
package. I'm following the instructions in its vignette. I used:

library(baySeq)
data(pairData)
pairCD <- new("pairedData", data = pairData[,1:4], pairData =
pairData[,5:8],replicates = c(1,1,2,2),groups = list(NDE = c(1,1,1,1), DE =
c(1,1,2,2)))

As it indicated, The first four columns in these data are paired with the
second four columns. So I think Sample 1-Sample 4 is group1 and Sample
5-Sample 8 is group2. And Sample 1 is paired with Sample 5, Sample 2 is
paired with Sample 6~~~
In the result, the most significant gene is the 5th row.  The result is:

   rowID   X1.1  X1.2     X2.1   X2.2 Likelihood  DE      FDR.DE
1      5 159:73 44:24     0:49   0:68  0.9974276 1>2 0.002572417

Its expression is:
159  44   0   0  73  24  49  68

It is very obvious that the software take 3th and 4 th samples (0,0) as
group 2, 7th and 8th samples (49, 68) as group 1, which is not correct.
So I am not very clear with the replicates = c(1,1,2,2) and DE =
c(1,1,2,2). What do they mean here? What is the correct method to do paired
data analysis in baySeq package?

Thank you!

Best,
Shilin

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