User: panagiotis.mokos

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Posts by panagiotis.mokos

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Problem about functional annotation network of WGCNA modules (modified)
... Dear Bioconductor users, I am working with TCGA RNA-seq data. I performed WGCNA analysis using vst transformed data and I found 13 network modules. To explore whether the most significant representatives (module membership (kME)>=0.7) in each module share a common biological function, I performe ...
wgcna pathway analysis network analysis written 2.3 years ago by panagiotis.mokos • 30
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Problem about module preservation statistics in WGCNA software
... Dear Bioconductor users, I am working with TCGA RNA-seq data. I performed WGCNA analysis using vst transformed data and I found 13 network modules. Now I want to perform module preservation analysis using as reference and test sets the same data in order to check the robustness of module definition ...
rnaseq wgcna tcga written 2.5 years ago by panagiotis.mokos • 30
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Comment: C: Problem about use of TCGA rna-seq rsem gene results for regularized cox regressi
... Dear Love, Thank you very very much for your response!! Sincerely, Panagiotis ...
written 2.6 years ago by panagiotis.mokos • 30
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Comment: C: Problem about use of TCGA rna-seq rsem gene results for regularized cox regressi
... Dear Love,  Thank you very much for your response. Could you explain more the differences between the above-mentioned scatterplots (ie between the rlog and VST method)? Also what happens about the variance of lowly expressed genes between rlog and VST transformation (given that the mean values of l ...
written 2.6 years ago by panagiotis.mokos • 30
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Comment: C: Problem about use of TCGA rna-seq rsem gene results for regularized cox regressi
... Dear Love, I have just read in detail your  RNA-seq workflow from this link http://www.bioconductor.org/help/workflows/rnaseqGene/#the-deseqdataset-sample-information-and-the-design-formula. At some point you refer "While the rlog is on roughly the same scale as the log2 counts, the VST has a upwar ...
written 2.6 years ago by panagiotis.mokos • 30
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How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
... Dear Bioconductor users, I am working with TCGA RNA-seq data. I have downloaded the rsem.genes.result file for a specific cancer type  and I've understood that the "raw_count" is the estimated number of fragments derived from a given gene and the "scaled_estimate" is the fraction of transcripts mad ...
rnaseq normalization R tcga rsem written 2.6 years ago by panagiotis.mokos • 30
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Comment: C: About rsem.genes.results of TCGA RNA-seq v2 and normalization strategies
... Dear Love, I aggree with you. Thank you very much!! Panagiotis ...
written 2.6 years ago by panagiotis.mokos • 30
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Comment: C: Problem about use of tcga rna-seq rsem gene results for regularized cox regressi
... Dear Love, I have read the paper here "Charlotte Soneson, Michael I. Love, Mark D. Robinson (2015): Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research"  and the tximport vignette. In this pipeline you note that  there are two suggested ways of ...
written 2.6 years ago by panagiotis.mokos • 30
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Comment: C: Problem about use of tcga rna-seq rsem gene results for regularized cox regressi
... Dear Love, Thank you very very much for your quick and informative reply!! Panagiotis ...
written 2.6 years ago by panagiotis.mokos • 30
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Comment: C: Problem about use of tcga rna-seq rsem gene results for regularized cox regressi
... Dear Love, Thank you very much for your response! Just a little correction.The phrase in the brackets is not "which to use" but "why to use".  In  varianceStabilizingTransformation R documentation is refered that the transformations performed from this function are useful when checking for outlie ...
written 2.6 years ago by panagiotis.mokos • 30

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Problem about picking soft threshold power in WGCNA software
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Problem about picking soft threshold power in WGCNA software
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
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