User: user56

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user5610
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Posts by user56

<prev • 6 results • page 1 of 1 • next >
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Comment: A: WGCNA for different comparisons
... Thank you very much for your help, that's exactly what I needed! ...
written 29 days ago by user5610
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Problem with ModuleSignificance - how to filter genes?
... While using this code in WGCNA: dynamicMods = cutreeDynamic(dendro = geneTree, distM = dissTOM, deepSplit = 2, pamRespectsDendro = FALSE, minClusterSize = minModuleSize); dynamicColors = labels2colors(dynamicMods) GS1= as.numeric(c ...
wgcna modulesignificance written 4 weeks ago by user5610 • updated 4 weeks ago by h.mon21k
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WGCNA for different comparisons
... Since I've just started my analysis using WGCNA, I'm not really familiar with it so far. I need to do different comparisons in WGCNA. I have two ethnicities, for each of them I have three comparisons group, let's say A, B , C and among each of these, three classes (class1, class2, class3). For now, ...
wgcna rna-seq written 4 weeks ago by user5610
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Comment: C: RNA-Seq normalization using limma or DESeq2
... Thank you very much! I'm just thinking, because of the time it takes to run vst in WGCNA, if I could use both of them on different kinds of analysis (varianceStabilizingTransformation for PCA, up/downgenes heatmpas, fgsea and getVarianceStabilizedData for WGCNA). Why do you prefer rlog? What is th ...
written 7 weeks ago by user5610
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Comment: C: RNA-Seq normalization using limma or DESeq2
... Thank you. My data seems to be pretty noisy. Also, is it ok to use only DESeq2 without any other steps like vst? ...
written 7 weeks ago by user5610
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RNA-Seq normalization using limma or DESeq2
... Hello, I just started analysis of RNA Seq Data (bulk - whole genome). I was trying to normalize data using limma package (voom). Is it correct to create a DGE list, then use calcNormFactors (method TMM) and then voom (normalize = none)? I've went through different papers, but I'm not really sure wh ...
normalization limma rna-seq dseq2 written 7 weeks ago by user5610

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