User: sarahmacdonald86

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Posts by sarahmacdonald86

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Comment: A: DESeq2 in phyloseq
... Hi Michael, Thanks for the clarification. Changing from using numerical values for LesionScore in my mapping file fixed the problem (eg from 4 to four etc), meaning I guess this is now coded as a factor. Cheers, Sarah ...
written 20 months ago by sarahmacdonald860
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DESeq2 in phyloseq
... Hello, I am using DESeq2 in phyloseq to analyse my data, following the phyloseq tutorial. Previously I used the following code and this seemed to work nicely, however when I am trying to repeat this I now get the following message and although the listed bacterial species are the same the log2fold ...
phyloseq deseq2 written 20 months ago by sarahmacdonald860
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Controlling colours assigned to order in DeSeq2 plot in phyloseq
... Hello, I am following the DeSeq2 tutorial in Phyloseq and I'm using the following code to plots OTUs by Genus, coloured by Order. I am doing multiple plots, which I want to then group together and the problem is that because some have different Orders included there is no colour consensus over the ...
phyloseq ggplot2 color written 20 months ago by sarahmacdonald860 • updated 20 months ago by Michael Love20k
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Comment: C: Problem reproducing PCA plot in DeSeq2 totuorial
... Hi Michael, Yes this seemed to be the problem, loaded a new session with only the packages I needed and this worked. Thanks everyone.  ...
written 22 months ago by sarahmacdonald860
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Comment: C: Problem reproducing PCA plot in DeSeq2 totuorial
... Sorry yes, better to add comment. > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12 locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel  stats4    stats     gra ...
written 22 months ago by sarahmacdonald860
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Comment: A: Problem reproducing PCA plot in DeSeq2 totuorial
... Hi James, I tried this and simply get this: [1] TRUE Help! cheers, Sarah ...
written 22 months ago by sarahmacdonald860
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Problem reproducing PCA plot in DeSeq2 totuorial
... Hello, I am following the Differential analysis of count data – the DESeq2 package vignette which is great, however when I come to and can produce heatmaps, however when i try a PCA plot i get the following error. plotPCA(rld, intgroup=c("LesionScore", "Treatment") Error in (function (classes, fd ...
deseq2 pca plot written 22 months ago by sarahmacdonald860

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