User: 王喆

gravatar for 王喆
王喆60
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9 years, 1 month ago
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9 years, 2 months ago
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z*********@yahoo.cn

Posts by 王喆

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Clustering RNA-seq profiles and DE analysis using edgeR
... Dear Gordon,  Thank you very much. Your answers help me a lot. Best wishes, Zhe Dear Zhe, On Thu, July 1, 2010 1:58 pm, ?? wrote: > Dear Gordon, > > I tryed plotMDS.dge function and got good results. But I have two questions: > > 1. What do "Dimension 1" and "Dimension 2" repres ...
written 9.2 years ago by 王喆60
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Answer: A: Clustering RNA-seq profiles using edgeR
... Dear Gordon,  I tryed plotMDS.dge function and got good results. But I have two questions:  1. What do "Dimension 1" and "Dimension 2" represent, respectively?  2. I have 12 different samples which were collected from 3 different positions of an organ from 2 species at 2 stages (3*2*2=12 samp ...
written 9.2 years ago by 王喆60
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Comment: C: edgeR normalization factors
... Thank you for your suggestions. Zhe --- 10年6月29日,周二, Naomi Altman 写道: 发件人: Naomi Altman 主题: Re: [BioC] edgeR normalization factors 收件人: "Mark Robinson" , "Naomi Altman" 抄送: "王喆" , bioconductor@stat.math.ethz.ch 日期: 2010年6月29日,周二, ...
written 9.2 years ago by 王喆60
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Comment: C: edgeR normalization factors
... Thanks Mark and have a good trip. Zhe --- 10年6月29日,周二, Mark Robinson 写道: (Travelling so this is a rather quick response) I disagree with Naomi. First, for a differential expression analysis, we prefer to use the counts as is, and use the normalization factors as offsets in t ...
written 9.2 years ago by 王喆60
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edgeR normalization factors
... Hello,  I have a question about using TMM normalization factors. I want to modify the count for each gene after normalization. Should I just need to divide the count of each gene by the normalization factor for its library? Then, I may use the normalized data for DE analysis and other further anal ...
normalization written 9.2 years ago by 王喆60 • updated 9.2 years ago by Naomi Altman6.0k
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edgeR question
... Hello,  I am learning edgeR and would like to use it dealing with my Tag-seq and RNA-seq data. I have several questions:  1. Does the DE analysis using common dispersion or moderated tagwise dispersions use the TMM method for normalization?  I am not sure the relationship between Setion 6 ...
edger written 9.2 years ago by 王喆60 • updated 9.2 years ago by Gordon Smyth38k

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