User: Mau

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Mau20
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3 years, 2 months ago
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Posts by Mau

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Minimum number of samples per treatment/group for WGCNA analysis
... Thank you for your answer agustin.gonvi. In an experiment with 15 samples and 2 groups, each group will have 7-8 samples if they are evenly distributed, so I guess it would be OK to keep that sample size with three treatments, for a total of 21-24 samples. ...
written 5 months ago by Mau20
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Comment: C: Minimum number of samples per treatment/group for WGCNA analysis
... Thank you for your input ravisaroch, but could you elaborate a bit? The links I posted say that you need 15 samples total (treatment + control), and I an interested in an experimental design with more than two groups. Thanks ...
written 5 months ago by Mau20
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Minimum number of samples per treatment/group for WGCNA analysis
... Hi, I am in the process of designing an RNA-seq experiment with a non-model organism. I would like to have 3 treatments/groups, and analyze my data with a gene coexpression network analysis like WGCNA. Despite extensive searching, I am still dubious about how many samples I need. I know that I sh ...
wgcna rna-seq gcn gene coexpression network written 5 months ago by Mau20 • updated 5 months ago by agustin.gonvi10
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Comment: C: TopGO - GenTable parameters
... I would also like to know how to get full GOterms from GenTable, instead of truncated ones ...
written 12 months ago by Mau20
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Comment: C: bug in estimateDisp() or mistake in documentation?
... Sorry to post on such an old question, but I am facing the same situation. I am trying to use the classic method, and I get different results when using estimateDisp   vs   estimateCommonDisp + estimateTagwiseDisp. Am I correct to assume that estimateDisp is the best option? Thanks Mau   ...
written 16 months ago by Mau20
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Comment: C: Is the CPM filtering method from NOISeq unsupervised?
... Thanks for your input. I agree with your general rule, but isn't the criteria I asked about breaking it? It seems to me that it filters based on expression levels within each condition (group) ...
written 2.2 years ago by Mau20
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Is the CPM filtering method from NOISeq unsupervised?
... Hi, Previous questions (for example here or here) and at least this paper have stressed the importance of using unsupervised filtering methods for lowly expressed genes in a DE analysis. To my understanding, this means that such filters must have no knowledge of which condition is applied to each s ...
rnaseq noiseq gene filtering de analysis written 2.2 years ago by Mau20 • updated 2.2 years ago by James W. MacDonald51k
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Comment: A: Why does the filtering of lowly expressed genes for analysis with edgeR must be
... Thank you both for your replies. I read the paper and I was able to grasp the basics. I wonder if it is possible to apply a desired filter and then somehow test if "the conditional and unconditional null distributions of Ui-II are the same."  I was thinking that this could serve as a way to argue f ...
written 3.2 years ago by Mau20 • updated 3.2 years ago by Gordon Smyth39k
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Why does the filtering of lowly expressed genes for analysis with edgeR must be done unsupervised?
... Hi, Like many others, I have struggled choosing the most adequate filtering parameters for lowly expressed genes in a DE analysis. I would like to filter out genes that don't meet a minimum expression threshold within all samples from each condition. This idea was expressed in the comments of this ...
rnaseq edger gene filtering de analysis written 3.2 years ago by Mau20

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