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 4 months ago by panagiotis.mokos10
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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 7 months ago by panagiotis.mokos10
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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 8 months ago by panagiotis.mokos10
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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 8 months ago by panagiotis.mokos10
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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 8 months ago by panagiotis.mokos10
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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 8 months ago by panagiotis.mokos10
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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 8 months ago by panagiotis.mokos10
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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 8 months ago by panagiotis.mokos10
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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 8 months ago by panagiotis.mokos10
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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 8 months ago by panagiotis.mokos10

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