[BioC] a problem with DESeq

wang peter wng.peter at gmail.com
Mon Sep 17 17:08:23 CEST 2012

i have two sample, one is wild, the other is mutant
i met a very wired problem
when i set parameter sharingMode = "fit-only", such coding cannot work
but if i set sharingMode=default, it can work

and then i updated the packages, the problem still exists.


raw.data <- read.table("expression-qwei.txt",row.names=1)
counts <- raw.data[, 2:dim(raw.data)[2]]
length<-raw.data[, 1]
counts <- counts[rowSums(counts) >= length(conditions)/2,]
cds <- newCountDataSet(counts, conditions)
lib_size <- read.table("lib_size_qwei.txt");
lib_size <- unlist(lib_size)

cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds, method = "blind",sharingMode="fit-only")
> dispTable(cds)
[1] NA NA

cds <- estimateDispersions(cds, method = "blind")
> dispTable(cds)
 mutant    wild
"blind" "blind"

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

[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
[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_1.8.3         BiocInstaller_1.4.7 locfit_1.5-8
Biobase_2.16.0      BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] annotate_1.34.1      AnnotationDbi_1.18.1 DBI_0.2-5
genefilter_1.38.0    geneplotter_1.34.0
 [6] grid_2.15.1          IRanges_1.14.4       lattice_0.20-6
RColorBrewer_1.0-5   RSQLite_0.11.1
[11] splines_2.15.1       stats4_2.15.1        survival_2.36-14
tools_2.15.1         XML_3.9-4.1
[16] 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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