[BioC] DEXSeq without replicates?

Duke duke.lists at gmx.com
Thu Dec 22 21:41:29 CET 2011


Hi folks,

I am testing the DEXSeq package with a public RNA-Seq data. 
Unfortunately this data set does not have replicates, only two set of 
data with two conditions. I tried DEXSeq but got error. I checked the 
estimateDispersion function but there is no similar option like in DESeq 
where we can use for non replicate data. Is there any way to overcome 
this disadvantage of the data and finish the DEXseq analysis for it, or 
it is simply a no-go?

By the way, my sessionInfo() if that helps:

 > sessionInfo()
R Under development (unstable) (2011-12-12 r57875)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] DEXSeq_1.1.3       Biobase_2.15.3     BiocGenerics_0.1.3

loaded via a namespace (and not attached):
[1] hwriter_1.3    plyr_1.6       statmod_1.4.14 stringr_0.6
 >

Thanks in advance,

D.



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