5.9 years ago by
Assuming that the aim is to find differences between the primary and
recurrent data, the replicates parameter could be (for example)
the groups parameter
list(Agroup = as.factor(rep("A", 11))
i.e., they are all replicates, and you are not looking for
expression between patients. In the 'getLikelihoods.BB' function you
will then need to specify that 'nullProps = 0.5'; that is to say that
the 'null' model is for a fifty-fifty split of expression between
You can then use the 'topCounts' with 'group = "Agroup"' to see those
genes which differ from this model, and hence show consistent
differential expression across your samples.
On 18/09/13 16:08, alice [guest] wrote:
> I would like to run a paired baySeq analysis containing 11 pairs
(primary vs. recurrent), so a total of 22 samples. I am unsure of how
to specify the groups and replicates parameters in the "pairedData"
class. There is no other grouping parameter. They are all cases.
> -- output of sessionInfo():
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>  C
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  edgeR_3.0.8 limma_3.14.4 baySeq_1.12.0
> loaded via a namespace (and not attached):
>  tools_2.15.0
> Sent via the guest posting facility at bioconductor.org.
Dr. Thomas J. Hardcastle
Department of Plant Sciences
University of Cambridge
Cambridge, CB2 3EA