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! 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 hours 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 4 days 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 ...
rnaseq deseq2 differential gene expression written 9 days ago by engelbrecht.stephan10 • updated 8 days ago by Michael Love14k

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