User: aravenscraft

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Posts by aravenscraft

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[DESeq2] is it ok to remove contaminant/sparse OTUs prior to DESeq analysis?
... Hi! Quick question about the type of count data DESeq2 expects as input: Should I avoid doing any clean-up prior to normalizing my data with DESeq2?  Currently, I remove contaminant OTUs (those that were present in the extraction kit or PCR reagents) from my OTU table. I am also considering removin ...
deseq2 written 3.7 years ago by aravenscraft0 • updated 3.7 years ago by Ryan C. Thompson7.3k
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Answer: A: [DESeq2] normalization doesn't remove my mean-variance trend
... Thank you Ryan and Michael!  That helps me understand what is happening much better. I do have low sequencing depths, and my gut communities were both low diversity, and highly variable between individual insects.  The large number of low-abundance OTUs are likely stray bacteria that were just pass ...
written 3.7 years ago by aravenscraft0
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[DESeq2] normalization doesn't remove my mean-variance trend
... Hi all, I conducted a barcoded amplicon sequencing study to characterize the gut flora of butterflies subjected to different treatments.  I have an OTU table and I'm trying to learn to normalize the counts in it using DESeq2. Ultimately, I want to obtain normalized counts for downstream visualizati ...
normalization deseq2 plotma meansdplot written 3.7 years ago by aravenscraft0

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