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Mike Smith
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40
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110
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6
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1.7k
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460
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620
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3
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1.2k
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100
3
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12
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6.2k
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70
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0
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3
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1.6k
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270
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10
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willj
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30
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3
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1.1k
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Matt Ritchie
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460
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4
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2.3k
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Sean Davis
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Krys Kelly
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270
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4
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1.4k
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Mark Dunning
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320
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110
3
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9
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5.7k
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1.9k
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2
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60
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3
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1.5k
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50
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0
0
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4
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978
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460
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30
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5
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1.6k
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40
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10
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4
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1.7k
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1.1k
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0
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11
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10
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7
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60
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Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
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Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
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Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
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Hi,
I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation.
Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
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swbarnes2
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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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