[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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