User: panagiotis.mokos
panagiotis.mokos • 10
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Posts by panagiotis.mokos
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... 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 ...
written 22 days ago by
panagiotis.mokos • 10
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... 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 ...
written 3 months ago by
panagiotis.mokos • 10
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... Dear Love,
Thank you very very much for your response!!
Sincerely,
Panagiotis
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written 4 months ago by
panagiotis.mokos • 10
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... 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 4 months ago by
panagiotis.mokos • 10
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... 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 4 months ago by
panagiotis.mokos • 10
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... 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 ...
written 4 months ago by
panagiotis.mokos • 10
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... Dear Love,
I aggree with you.
Thank you very much!!
Panagiotis
...
written 4 months ago by
panagiotis.mokos • 10
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... 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 4 months ago by
panagiotis.mokos • 10
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... Dear Love,
Thank you very very much for your quick and informative reply!!
Panagiotis
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written 4 months ago by
panagiotis.mokos • 10
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... 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 4 months ago by
panagiotis.mokos • 10
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