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Answer: Identical samples after deseq2 batch effect removal
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Michael Love
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> 2 of my treatment samples have identical normalised gene expression for all genes.
This sounds like a quantification / sample labeling…
Answer: Downloading Metagenomic Data with Higher Taxonomic Units
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Levi Waldron
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I'm sorry I missed the first post! Yes, it is easy to agglomerate ranks in curatedMetagenomicData datasets. See the example in the vignette…
Comment: Differene between the Wald and LRT test for time-series gene expression data
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Denise
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This makes a lot of sense, thank you very much!
Comment: Downloading Metagenomic Data with Higher Taxonomic Units
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elozanoe
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Hi! I'm facing the same problem.
Is there any easy way to output relative abundances of higher taxonomic units (up to kingdom), similar to…
Comment: Is it recommended to analyze different tissues together when using edgeR
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Gordon Smyth
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Just plot the samples with plotMDS().
Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
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