[BioC] a possible bug in DESeq

[Wolfgang Huber]

Dear Shan Gao

thank you. I was not able to reproduce what you report, based on the 
code below and a different data set. Can you please send us the data 
file "expression-qwei.txt" (or any other data set that for you produces 
this problem) together with the exact code that you ran (e.g. according 
to the output of the R function 'history') ?

	Best wishes
	Wolfgang


On 7/29/12 5:13 PM, wang peter wrote:
> 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
>
>


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber