User: amgodogma

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amgodogma10
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Posts by amgodogma

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Comment: C: DirichletMultinomial Package Not Functioning
... Thanks Martin. That helped me identify the problem, 0s!!! ...
written 4 weeks ago by amgodogma10
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DirichletMultinomial Package Not Functioning
... Hi again I've been using the DirichletMultinomial package perfectly for the last couple of years and its been amazing so thank you to the devs. However, recently I've been getting an error when I run the following command: fit.all <- mclapply(1:7, dmn, count=count, verbose=TRUE) The error ...
dirichletmultinomial dmn written 4 weeks ago by amgodogma10 • updated 4 weeks ago by Martin Morgan ♦♦ 23k
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Comment: C: DESeq2 PCOA Plots
... Sorry I replied to the wrong comment. Yeah does anyone know of a back-conversion function or Is there a way I can calculate the distance matrix within the DESeq object? thanks ...
written 4 months ago by amgodogma10
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Comment: A: DESeq2 PCOA Plots
... HI Michael Thanks for your response. I know how to do it with a phyloseq object. But for the project I'm working on I have a DESeq2 object. thanks ...
written 4 months ago by amgodogma10
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DESeq2 PCOA Plots
... Hi all I was wondering if anyone had a pipeline for calculating distances by Bray-Curtis and plotting a PCOA plot with a DESeq2 object? The plotPCA function doesn't seem to give you the option to choose which distance metric to use. If anyone has any ideas/suggestions that would be very helpful ...
deseq2 written 4 months ago by amgodogma10
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Invalid class DESeqDataSet object with Phyloseq
... Hi everyone I am trying to use DESeq2 on a Phyloseq object and am running into a consistent error. I've followed all the online tutorials, however whenever I get to the stage to run "phyloseq_to_deseq2" I get the following error: invalid class “DESeqDataSet” object: levels of factors in the desi ...
phyloseq deseq2 written 12 months ago by amgodogma10 • updated 12 months ago by Michael Love24k
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Need Help Using DirichletMultinomial Package
... Hi all I am using the DirichletMultinomial package to identify clusters in an Airways Microbiome dataset. In a PCOA analysis I can see 2 clear clusters buy when I run the DMM package I'm told the best model is with one cluster? I've tried this with 3 different datasets now and I keep getting one c ...
dirichletmultinomial dmm written 2.3 years ago by amgodogma10 • updated 2.3 years ago by Martin Morgan ♦♦ 23k

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