[BioC] a possible bug in DESeq

[wang peter]

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


rm(list=ls())
library(DESeq)

raw.data <- read.table("expression-qwei.txt",row.names=1) #
counts <- raw.data[, 1:dim(raw.data)[2]]#
conditions=c("mutant","wild") #
counts <- counts[rowSums(counts) >= length(conditions)/2,]#
cds <- newCountDataSet(counts, conditions)#

#normalization
cds <- estimateSizeFactors(cds)
sizeFactors(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)

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
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

loaded via a namespace (and not attached):
 [1] annotate_1.32.3       AnnotationDbi_1.16.19 DBI_0.2-5
genefilter_1.36.0     geneplotter_1.32.1    grid_2.15.1
IRanges_1.12.6
 [8] lattice_0.20-6        RColorBrewer_1.0-5    RSQLite_0.11.1
splines_2.15.1        survival_2.36-14      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