User: engelbrecht.stephan

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Posts by engelbrecht.stephan

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Comment: C: Allele Specific Expression Using edgeR
... Hi Aaron, last question on this (I really appreciate you coming back to this old thread): I have four genotypes, with varying heterozygosity - the same gene may have 5 SNPs in one genotype, but 10 SNPs in another. My gene counts are composed of adding phased allelic counts across multiple SNPs toge ...
written 12 weeks ago by engelbrecht.stephan10
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Comment: C: Allele Specific Expression Using edgeR
... Hi Aaron, Thank you for your rapid response and for filling in the gaps to my vague question. The reason why I was asking was indeed because I have four genotypes, not two. I suspected that this was the case, but just wanted to make sure. Thanks so much! ...
written 8 months ago by engelbrecht.stephan10
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Comment: C: Allele Specific Expression Using edgeR
... Hi Aaron, I hope it is suitable to expand on this experimental design a bit. I have a study design similar to this, but in addition to contrasting ASE in different groups, I would like to test if the genotype has a significant effect on the degree of ASE across all individuals. So I would like to c ...
written 8 months ago by engelbrecht.stephan10
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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 10 months 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 10 months 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 11 months 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 11 months 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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