[BioC] report a problem of DESeq

[wang peter]

hello all:
        i run a scipts to deal with my data.
every thing is ok, but the last step generate some
wired lines

rm(list=ls())
library(DESeq)
raw.data <- read.table("ordered_sense_raw_v2.csv",row.names=1)
counts <- raw.data[, 1:dim(raw.data)[2]]
conds = c(rep("col15",3),rep("col1",3),rep("col2h",3),rep("col30",3),rep("col6h",3),rep("flu15",3),rep("flu1",3),rep("flu2h",3),rep("flu30",3),rep("flu6h",3))
counts <- counts[rowSums(counts) >= length(conds)/2,]
cds <- newCountDataSet( counts, conds )
cds <- estimateSizeFactors(cds)
sizeFactors(cds)
cds <- estimateDispersions(cds)
et <- nbinomTest(cds, "col6h", "flu6h")
etSig <- et[et$padj < 0.05, ]


etSig have some lines, like this
no id

          id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
NA.4649 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.4650 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.4651 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.4652 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.4653 <NA>       NA        NA        NA         NA             NA   NA   NA
NA.4654 <NA>       NA        NA        NA         NA             NA   NA   NA--

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

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

other attached packages:
[1] DESeq_1.6.1         locfit_1.5-8        Biobase_2.14.0
BiocInstaller_1.2.1

loaded via a namespace (and not attached):
 [1] annotate_1.32.3       AnnotationDbi_1.16.19 DBI_0.2-5
genefilter_1.36.0
 [5] geneplotter_1.32.1    grid_2.14.1           IRanges_1.12.6
lattice_0.20-0
 [9] RColorBrewer_1.0-5    RSQLite_0.11.1        splines_2.14.1
survival_2.36-10
[13] tools_2.14.1          xtable_1.7-0

shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu
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