[BioC] bayseq pair data

Tom Hardcastle tjh48 at cam.ac.uk
Wed Sep 18 17:40:27 CEST 2013


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



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