[BioC] report a possible bug of edgeR

[wang peter]

i have two group of samples,
each group have 3 biological replicate
library(edgeR)
library(limma)

raw.data <- read.table("111",row.names=1)
d <- raw.data[, 1:dim(raw.data)[2]-1
group <- factor(c(rep("sap", 3),rep("vas", 3)))
d <- DGEList(counts = d, lib.size =
c(9893630,11055814,11207084,9663487,11455088,8140053), group = group)
d <- d[rowSums(d$counts) >= length(group)/2,]

#normalization
d <- calcNormFactors(d)

#To estimate common dispersion:
d <- estimateCommonDisp(d)
#To estimate tagwise dispersions:
d <- estimateTagwiseDisp(d)

et <- exactTest(d)
result <- topTags(et, n=dim(d)[1]+1, adjust.method="BH", sort.by="logFC")
write.table(result,file = "DEresult",sep = "\t")

Error in data.frame(table = list(logConc = c(-30.7452523676841,
-30.9164328563752,  :
  arguments imply differing number of rows: 92305, 1, 2

but write.table(result[1:92304,],file = "DEresult",sep = "\t") can work well
and then result[92305,] can also work well:

           logConc         logFC P.Value FDR
UN089145 -16.96614 -4.874874e-05       1   1


another problem is the result file
"table.logConc"	"table.logFC"	"table.P.Value"	"table.adj.P.Val"	"adjust.method"	"comparison"
"UN038758"	-30.7452523676841	-38.5416037522595	1.78446331842105e-37	2.74524811011424e-33	"BH"	"sap"


"comparison" should include two group name like, "sap" vs "vas"
but why only one name?

-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
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