User: carlgdeboer

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Posts by carlgdeboer

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Comment: C: EdgeR: batches and samples over-specify system, how to contrast un-modeled varia
... Awesome! Thanks for pointing me in the right direction.  Much appreciated! ...
written 4.2 years ago by carlgdeboer0
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Comment: C: EdgeR: batches and samples over-specify system, how to contrast un-modeled varia
... If you are looking at age-specific effects across all cell types and time points, then yes, you are correct.  However, if it is an age/cell type/time point specific effect then it may still be evident as only effects that are consistent across an age will have been normalized out (or the effect will ...
written 4.2 years ago by carlgdeboer0
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Comment: C: EdgeR: batches and samples over-specify system, how to contrast un-modeled varia
... Hi Gordon Thanks for the reply and for correcting me on the workaround.  I'm afraid I don't really understand why mice cannot be treated as batches.  Since we have two biological replicates, I would think we could learn one weight for each mouse, which brings all the samples from those mice on the ...
written 4.2 years ago by carlgdeboer0
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Comment: A: EdgeR: batches and samples over-specify system, how to contrast un-modeled varia
... I have partly solved the problem.  If I want the following contrast: young_MPP_0.5vs0 = Gyoung_MPP_0 - Gyoung_MPP_0.5, but Gyoung_MPP_0 is not represented in the design matrix, I can just do  young_MPP_0.5vs0 = - Gyoung_MPP_0.5, I still don't know how to compare two variables that are bo ...
written 4.2 years ago by carlgdeboer0 • updated 4.2 years ago by Gordon Smyth38k
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EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
... Hi All I am trying to find differentially expressed genes with edgeR, while simultaneously accounting for batch effects.  Unfortunately, the batches completely encompass the samples, so that if I specify the batches and the samples in my edgeR design matrix, the system is over-specified (i.e. there ...
edger design and contrast matrix differential expression glmlrt() written 4.2 years ago by carlgdeboer0 • updated 4.2 years ago by Gordon Smyth38k

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