User: xr2120

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xr21200
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Posts by xr2120

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Comment: C: DESeq2 why estimate dispersion on log scale
... Thank you so much for the detailed explanation.  ...
written 11 weeks ago by xr21200
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DESeq2 why estimate dispersion on log scale
... Hi,  I have a question about how DESeq2 estimate dispersion parameters. In the low level function of DESeq2, when estimating dispersion alpha, I think the function is optimizing alpha on log scale (i.e. take the partial derivative with respect to log(alpha)). My questions are: 1. Why not optimizin ...
deseq2 estimatedispersions dispersoin written 11 weeks ago by xr21200 • updated 11 weeks ago by funnyjokes1.com0
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Comment: C: gseDO function input
... Hi Guangchuang, Thanks for your prompt response. I have figured out this issue. I checked your GitHub page, and noted that gseDO permutates the gene list to get empirical distribution of ES. I thought it permutates phenotypes. That's why I get confused. Thanks for your help.        ...
written 11 months ago by xr21200
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gseDO function input
... Hi all, I'm a little bit confused about the input of gseDO. In DOSE vignette, the input of gseGO is a gene list called "geneList". In this gene list, for each gene, there is a corresponding log fold change. But how can we calculate the correlation between each gene and phenotype if the input is jus ...
clusterprofiler dose written 11 months ago by xr21200 • updated 11 months ago by Guangchuang Yu1.0k

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