[BioC] weired bayseq results

[Fatemehsadat Seyednasrollah]

Just I forgot to mention that the order of replicates in the count table has changed in each rerun process.
And below is the my code:

function (table, each, samplesize) 
{
    counttable <- read.delim(table, header = FALSE, row.names = 1)
    replicates <- c(rep("control", each), rep("treatment", each))
    groups <- list(NDE = rep(1, (2 * each)), DE = c(rep(1, each), 
        rep(2, each)))
    counttable <- as.matrix(counttable)
    CD <- new("countData", data = counttable, replicates = replicates, 
        groups = groups)
    CD at libsizes <- getLibsizes(CD)
    cl <- NULL
    CD <- getPriors.NB(CD, samplesize = samplesize, estimation = "QL", 
        cl = cl)
    CD <- getLikelihoods.NB(CD, pET = "BIC", cl = cl)
    print("estProps: ")
    print(CD at estProps)
    return(CD)
}

Fatemeh
________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Fatemehsadat Seyednasrollah [fatsey at utu.fi]
Sent: Monday, November 19, 2012 2:14 PM
To: bioconductor at r-project.org
Subject: [BioC] weired bayseq results

Dear list,

I have used BaySeq to my RNA-Seq data to extract DE genes and I have several biological replicates for each condition(20 replicates for each condition). The point is that if I rerun the BaySeq over my dataset then the number of detected genes with a specific common FDR will change. Can it be possible?
For 10 times rerunning the script the number of detected genes with FDR < 0.05 are :
82, 85, 84, 87, 85, 85, 84, 86, 82, 83

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] baySeq_1.12.0

loaded via a namespace (and not attached):
[1] tools_2.15.1

Thank you in advance

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