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.
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
