User: engelbrecht.stephan

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Posts by engelbrecht.stephan

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Comment: C: SNP-level Allele-specific expression detection using DESeq2 in an unpaired exper
... Hi Michael Thanks, I though it had to be something like that, I guess I just (still) don't completely grasp the input and output of every function :). This makes sense, but I run into the following problem - It seems that adding estimateVar = FALSE means dispFit is not added to the metadata of dds ...
written 6 weeks ago by engelbrecht.stephan10
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Answer: A: SNP-level Allele-specific expression detection using DESeq2 in an unpaired exper
... Hi Michael. I apologise, I was a bit confused by your suggestion. but after going through the DESeq2 manual I came up with the following solution for obtaining MAP dispersion estimates: I created a placeholder dataset with matrix counts generated by makeExampleDESeqDataset, to which dispersion esti ...
written 7 weeks ago by engelbrecht.stephan10
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Comment: C: SNP-level Allele-specific expression detection using DESeq2 in an unpaired exper
... Hi Michael! Yes, I think the hacking is going to more effort than what it's worth. I'm pretty new at this, but what would you think of specifying the design matrix and counts data to glm.nb(), and a maximum likelihood approach can then be used to estimate the overdispersion parameter from all allel ...
written 8 weeks ago by engelbrecht.stephan10
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Comment: C: SNP-level Allele-specific expression detection using DESeq2 in an unpaired exper
... Hi Michael Thank you for your rapid response! Unfortunately I'm unable to rbind 'dds' experiments together, since the number of samples assayed for each haplotype 'condition' varies across genes/SNPs. Rbinding SummarizedExperiments requires that objects must have the same number of samples.  I don ...
written 9 weeks ago by engelbrecht.stephan10
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SNP-level Allele-specific expression detection using DESeq2 in an unpaired experimental design
... Hi, I'm interested in ASE in plant hybrids, of which I have an F2 backcross. F2 hybrid progeny can have both homospecific (or intra) or heterospecific (inter) haplotype combinations. At the same SNP, I will have some individuals that are both heterospecific, and homospecific, most often in unequal p ...

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