User: modarzi

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modarzi20
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Posts by modarzi

<prev • 68 results • page 1 of 7 • next >
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Dear Dr. Blighe Thanks for your comment. based on your guide I have decreased my data dimension from 56000 to 27000. but in 56000 dimension, I had 95 modules and now I have 141 modules. is this situation normal? I appreciate if you share your comment with me. Best Regards, Mohammad ...
written 6 days ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Dear Dr. Blighe Thanks for your comment. based on your good recommendation cutoff, MyData has decreased to 27251 genes. So, could you please give me reference for below formula: min + ((max-min) / 2) Best Regards, Mohammad ...
written 6 days ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Thanks for your comment. I filter MyData based on your suggestion code: filter <- which(apply(MyData, 1, var) > 0.2) But size of rows(genes) decrease from 56963 to 50580 and also it is high(50580). So, My question is how can I find best threshold for filtering? now this threshold is 0.2. ...
written 6 days ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Thanks for your comment. I have to remove genes based on low variance. So, for that purpose I need good function. during search in Internet I found 'genefilter' package in R. But, this package is useful when your data set is micro Array based on that vignette. Could you pleased suggest good solutio ...
written 7 days ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Dear Dr. Bleghe I want to use network approach for Identifying hub genes and pathways in 2 cancer. My data set was downloaded from TCGA and as you know typically all data sets in TCGA have more than 60000 gene type. So, If you want to construct network via these data set you face by high dimension ...
written 8 days ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Dear Dr. Blighe Thanks for your comment. based on your guide I have to filter some rows (gene expression data) based on variance cut-offs. So, If I think true about this filter, how can I determine this cutoffs? I appreciate if you share your comment with me. Best Regards, Mohammad ...
written 8 days ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... yes, I am trying to create a network from the entire data-matrix. dimension of my datExprSTLMS is 53 * 56900. if my process has problem based on which logic restriction I can filter my data set? Best Regards, Mohammad ...
written 9 days ago by modarzi20
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Comment: C: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Dear Dr. Blighe thanks for your comment. But for limitation in my hardware resource, I selected 'Automatic, one-step network construction and module detection' as an feasible option. But for importing my constructed network to Cytoscape, I have to use TOM. also for this purpose, I ran below code: ...
written 9 days ago by modarzi20
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Comment: C: data pre-processing for WGCNA Algorithm
... Dear Dr. Blighe Thanks for your comment. As you know I run WGCNA for my study.Now, I want to import my network in Cytoscape for visualization. based on WGCNA tutorial, for that purpose I have to run below code: # select modules modules = c("blue","brown") # Select module probes inMod ...
written 9 days ago by modarzi20
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problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
... Hi, I run WGCNA for my study.Now, I want to import my network in Cytoscape for visualization. based on WGCNA tutorial, for that purpose I have to run below code: # select modules modules = c("blue","brown") # Select module probes inModule=is.finite(match(moduleColorsFemale,modules)) ...
wgcna rna-seq topological overlap matrix written 11 days ago by modarzi20 • updated 9 days ago by WouterDeCoster30k

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