User: sebastian.lobentanzer

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Posts by sebastian.lobentanzer

<prev • 6 results • page 1 of 1 • next >
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Comment: C: ROC curves using normalized sequencing data from 2 experiments
... Hi Michael, thanks for the rapid help! I think my question might not have been clear enough; anyhow, the pseudocounts do next to nothing to the genes I am interested in for the ROC, probably because these are some of the most highly expressed genes in the set. I updated my question accordingly, c ...
written 15 days ago by sebastian.lobentanzer10
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ROC curves using normalized sequencing data from 2 experiments
... Hi all, hi Michael, we want to build receiver operating characteristics for patients from two separate cohorts (using gene expression from sequencing as predictor), and I was thinking about how to compare them in this context. I did vst() (`varianceStablilizingTransformation()`) on both of them and ...
deseq2 glm proc rocr written 15 days ago by sebastian.lobentanzer10
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Comment: C: Correlate WGCNA modules from 2 separate analyses (small and large RNA)
... Thank you Peter, it worked perfectly! Your package is a work of art. ...
written 3 months ago by sebastian.lobentanzer10
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Correlate WGCNA modules from 2 separate analyses (small and large RNA)
... Hello everybody, this is a general question based on a practical problem: can something meaningful be derived from any kind of correlation between two separate WGCNA analyses of the same data (samples)? To illustrate: we have sequenced small and long RNA of patients and controls (separately from th ...
wgcna written 3 months ago by sebastian.lobentanzer10 • updated 3 months ago by Peter Langfelder2.1k
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Answer: A: DESeq2 error when creating the DESeqDataSet
... Solution: I recompiled all Bioconductor packages with source("https://bioconductor.org/biocLite.R") pkgs <- rownames(installed.packages()) biocLite(pkgs, type="source") and then restarted. ...
written 2.6 years ago by sebastian.lobentanzer10
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DESeq2 error when creating the DESeqDataSet
... I am trying to create a DESeqDataSet from a SummarizedExperiment. I am getting the error message: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assayNames’ for signature ‘"DESeqDataSet"’ While researching, I found this (verified) example to test wit ...

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Scholar 2.6 years ago, created an answer that has been accepted. For A: DESeq2 error when creating the DESeqDataSet

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