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updated 11.5 years ago by
Peter Glaus
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written 11.5 years ago by
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updated 8.7 years ago by
Ryan C. Thompson
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written 8.7 years ago by
Sam McInturf
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Peter Glaus
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951
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updated 9.0 years ago by
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written 9.0 years ago by
dietmar.pils
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Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
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Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
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Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed.
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