bayseq pair data
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@guest-user-4897
Last seen 9.6 years ago
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 baySeq • 1.1k views
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@thomas-j-hardcastle-3860
Last seen 6.5 years ago
United Kingdom
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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