Entering edit mode
wang peter
★
2.0k
@wang-peter-4647
Last seen 10.2 years ago
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),r
ep("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
Facebook:http://www.facebook.com/profile.php?id=100001986532253