Question: DEXSeq without replicates?
8.0 years ago by
Duke • 210
Duke • 210 wrote:
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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=C  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  DEXSeq_1.1.3 Biobase_2.15.3 BiocGenerics_0.1.3 loaded via a namespace (and not attached):  hwriter_1.3 plyr_1.6 statmod_1.4.14 stringr_0.6 > Thanks in advance, D.
ADD COMMENT • link •