>From what you are saying it sounds like you have meaningful data, and rows
containing all NAs in the output, try using

etSig <- et[ which(et$padj < 0.05), ]

to remove them.

which(is.na(et$padj < 0.05))

should identify the offending record rows to trace back what is happening
in your dataset.

Marcus


On Sat, Jul 7, 2012 at 7:19 AM, wang peter <wng.peter@gmail.com> wrote:

> 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@cornell.edu
> Facebook:http://www.facebook.com/profile.php?id=100001986532253
>
> _______________________________________________
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>

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