Question: bayseq pair data
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5.9 years ago by
Guest User12k
Guest User12k 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.
bayseq • 545 views
ADD COMMENTlink modified 5.9 years ago by Thomas J Hardcastle180 • written 5.9 years ago by Guest User12k
Answer: bayseq pair data
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5.9 years ago by
United Kingdom
Thomas J Hardcastle180 wrote:
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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