[BioC] bayseq pair data

[Tom Hardcastle]

Hi Alice,

Assuming that the aim is to find differences between the primary and 
recurrent data, the replicates parameter could be (for example)
as.factor(rep("A", 11))
the groups parameter
list(Agroup = as.factor(rep("A", 11))

i.e., they are all replicates, and you are not looking for differential 
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 pairs.

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.

Best wishes,

Tom

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.
>
> thanks
> alice
>
>   -- output of sessionInfo():
>
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics   grDevices utils     datasets methods   base
>
> other attached packages:
> [1] edgeR_3.0.8 limma_3.14.4  baySeq_1.12.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>
> --
> Sent via the guest posting facility at bioconductor.org.


-- 
Dr. Thomas J. Hardcastle

Department of Plant Sciences
University of Cambridge
Downing Street
Cambridge, CB2 3EA
United Kingdom