User: panagiotis.mokos

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Posts by panagiotis.mokos

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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 5 days ago by panagiotis.mokos0
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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 6 days ago by panagiotis.mokos0
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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 days ago by panagiotis.mokos0
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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 9 days ago by panagiotis.mokos0
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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 10 days ago by panagiotis.mokos0
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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 12 days ago by panagiotis.mokos0
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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 13 days ago by panagiotis.mokos0
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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 13 days ago by panagiotis.mokos0
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Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
... Dear Bioconductor users, I am working with TCGA RNA-seq data. I want to perform unbiased selection of features associated with overall survival of hepatocellular carcinoma patients using elastic net regularized cox regression modeling and then rank them by heir coefficient sizes. Me and my colleagu ...
rnaseq deseq2 voom tcga glmnet written 14 days ago by panagiotis.mokos0
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Comment: C: Normalization and transformation of RNA-seq raw data for regularized linear regr
... Dear Aaron, Thank you for your response! The main purpose of my analysis is to perform unbiased prediction and feature selection in high-dimensional survival regression applying bootstrap enhanced elastic net cox regression modeling. Although I use RNA-seq data to perform this analysis. Do you bel ...
written 15 days ago by panagiotis.mokos0

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