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 [[alternative HTML version deleted]]