[BioC] edgeR i get 377 significant genes where in DESeq i got 0

[papori [guest]]

Hi,
Assuming i have 2 files:
1's have 1,000,000 reads- one condition
2's have 3,000,000 reads- second condition

i used rsem for differential expression for each of the 2 files.

i used both programs to analyse differential expression.(edgeR & DESeq)

i have a problem in the results..(maybe you can help me..)
i used this manual http://manuals.bioinformatics.ucr.edu/home/ht-seq
so may script is that:

library("DESeq");
conditions <- c("1","2")
cds <- newCountDataSet(x,conditions)
cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds,method="blind",sharingMode="maximum",fitType="local")
res <- nbinomTest(cds,condA="1",condB="2")
res[order(res$padj), ][1:4,]

sigDESeq <- res[res$padj <= 0.05, ]
sigDESeq <- na.omit(sigDESeq)
sigDESeq <- as.character(sigDESeq[,1])

library("edgeR");
group <- factor(c(1,2))
cdsR <- DGEList(counts=x, group=group)
cdsR <- estimateCommonDisp(cdsR)
cdsR <- estimateTagwiseDisp(cdsR)
et <- exactTest(cdsR, pair=c("1", "2"))

all <- as.data.frame(topTags(et, n=100000))
sigedgeR <- all[all$adj.P.Val <= 0.05, ]
sigedgeR <- na.omit(sigedgeR)
sigedgeR <- row.names(sigedgeR)

source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/
My_R_Scripts/overLapper.R")
OLlist <- overLapper(setlist=list(DESeq=sigDESeq, edgeR=sigedgeR),
sep="_", type="vennsets")
counts <- sapply(OLlist$Venn_List, length)
vennPlot(counts=counts)
counts

oveLapp <- OLlist$Venn_List

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

i want to check Differential expression between biological replicates.
(here: i have only 2)
1 & 2 are biological replicates.

the problem is:
in edgeR i get 377 significant genes where in DESeq i got 0 (ZERO)

it looks weird to me, but i do'nt know what i did wrong..

Do you know?


Thanks,
Pap

 -- output of sessionInfo(): 

R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] edgeR_2.4.3  limma_3.10.2

loaded via a namespace (and not attached):
 [1] annotate_1.32.1       AnnotationDbi_1.16.16 Biobase_2.14.0        DBI_0.2-5             DESeq_1.6.1          
 [6] genefilter_1.36.0     geneplotter_1.32.1    grid_2.14.0           IRanges_1.12.6        RColorBrewer_1.0-5   
[11] RSQLite_0.11.1        splines_2.14.0        survival_2.36-12      tools_2.14.0          xtable_1.7-0   

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