User: c.oertlin

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c.oertlin0
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Posts by c.oertlin

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Comment: C: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
... That is what I was trying but I had the exact same problem with the "Model matrix not full rank". I found an issue in my colData and now it worked as far as I can tell. Thanks for the help and patience!   ...
written 3.2 years ago by c.oertlin0
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Comment: C: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
... I tried to restart the R session and it worked. There were phantom packages, which showed up in the sessioninfo() but were not actually loaded... after detaching them all worked fine. Do I apply the right lists in the contrast to get the contrast for fractionA/fractionB or in my case Polysome/Cytos ...
written 3.2 years ago by c.oertlin0
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Comment: C: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
... Hey Micheal, thanks for redirecting me to this post. I tried to apply DESeq2 in this way to my polysome profiling data. However I am running into an issue and a question. First of all the issue, it has to do with extracting the contrast of interest. Since it did not work with my data I tried to ru ...
written 3.2 years ago by c.oertlin0
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Comment: C: Covariates in DESeq2 for Polysome profiling Data
... We want to test differential translation in polysome profiling data. To assess this Polysome associated mRNA counts have to be corrected for cytosolic mRNA counts. An idea was to run a per gene DESeq analysis with different model parameters each time. So for a dataset containing X genes, run X DESeq ...
written 3.3 years ago by c.oertlin0
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Covariates in DESeq2 for Polysome profiling Data
... Dear Micheal, We are want to use DESeq2 using gene specific covariates (i.e. a separate set of covariates for each gene; these are also count data with the identical characteristics as compared to the input RNAseq data) but are struggling in what would be the best way of doing this. We thought that ...
deseq2 written 3.3 years ago by c.oertlin0 • updated 3.2 years ago by marco.trizzino8310

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