User: panagiotis.mokos
panagiotis.mokos • 20
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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 17 months ago by
panagiotis.mokos • 20
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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 20 months ago by
panagiotis.mokos • 20
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... Dear Love,
Thank you very very much for your response!!
Sincerely,
Panagiotis
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written 21 months ago by
panagiotis.mokos • 20
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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 21 months ago by
panagiotis.mokos • 20
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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 21 months ago by
panagiotis.mokos • 20
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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 21 months ago by
panagiotis.mokos • 20
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... Dear Love,
I aggree with you.
Thank you very much!!
Panagiotis
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written 21 months ago by
panagiotis.mokos • 20
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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 21 months ago by
panagiotis.mokos • 20
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... Dear Love,
Thank you very very much for your quick and informative reply!!
Panagiotis
...
written 21 months ago by
panagiotis.mokos • 20
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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 21 months ago by
panagiotis.mokos • 20
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