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Recent Replies
Comment: DESeq2 on metagenome KO counts
by
ATpoint
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This statement makes zero sense in response to what I wrote.
Comment: DESeq2 on metagenome KO counts
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Aleksandra
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I focused on the fact that DESeq2 models overdispersion, but overlooked its implicit assumption: normalisation works when the main source o…
Comment: DESeq2 on metagenome KO counts
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Aleksandra
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Thank you very much. I mistakenly drew a superficial analogy. I equated KO counters with gene counters.
Comment: DESeq2 on metagenome KO counts
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Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts
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ATpoint
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The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
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I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions:
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(I apologise for my previous reply; I wanted to be as detailed as possible)
DESeq2 handles KO counts perfectly well. For a time-series des…
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Aleksandra
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I apologise for how that sounded; I wanted to be as detailed as possible.
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A comment on: "*Wonky analysis is possible even with open-source R libraries.*"
True - and arguably, the risk of a wonky analysis is actua…
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`Trailmaker` likely only supports Parse's evercode data. <br>
`BioTuring` does not appear to have published pricing. <br>
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Found a few more when I asked around. I have no idea how good or bad these are. If anyone has used these or knows more about these, feel fr…
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> I performed a standard proteomics screening workflow
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No, it's unrelated. Doublets in 10x happen if two cells get enclosed into the same GEM droplet. This has nothing to do with how flow cytome…
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Wow, thats too long. How much RAM does your machine have, it is likely swapping
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