User: brynedal

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Posts by brynedal

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Comment: C: t-statistic from various limma-approaches does not follow the theoretical distri
... In your simulation we see a nice deviance from the diagonal for the significant genes, just as I would expect.  What I instead observe in our data (and to some extent also in the two lower plots in the original post) is that there really is no deviance from the straight line of t-statistics. Below ...
written 11 days ago by brynedal0
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Comment: C: t-statistic from various limma-approaches does not follow the theoretical distri
... Hi Aaron, Of course only genes that are not affected should follow the theoretical null-distribution, that is why we use the theoretical as our null. I agree that if we compare cells in complete distress with healthy cells then almost all genes should be affected. The Smchd1 experiment is a perturb ...
written 18 days ago by brynedal0
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t-statistic from various limma-approaches does not follow the theoretical distribution
... Dear BioC, I'm testing various approaches to deal with our RNA seq data that has variability in sample quality, single outlying counts etc. I love limma and all the methods that are implemented within this package. Yet, when trying different approaches I've noticed that the moderated t-statistic do ...
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Comment: C: DESeq2: betaPrior changes significance dramatically
... > resultsNames(ddsIb1)  [1] "Intercept"       "pat_idP10"        ...    "visita"          [78] "visitb"          "response0" "response1" "T_after0"        "T_after1"        "P_after"  The fold changes are not identical, they appear to be twice the size when specifying the contrast: So where ...
written 7 months ago by brynedal0
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Comment: C: DESeq2: betaPrior changes significance dramatically
... Hi Michael, You are fenomenal at answering questions fast. Thank you. You are correct in that I made misstake in my code above, when betaPrior is False, it should be "visit_b_vs_a" instead of "visitb" just as you say, I've corrected it above (and did run the correct code).  But, using contrast as ...
written 7 months ago by brynedal0
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DESeq2: betaPrior changes significance dramatically
... Dear Helpful Strangers, I am running multiple different regressions in a rather complex material. I am using DESeq2_1.12.4. I have noticed that using betaPrior=T or betaPrior=F makes a huge difference.  As far as I understand using betaPrior means that the log fold changes are shrunken, and these ...
deseq2 significance betaprior shrinkage written 7 months ago by brynedal0
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Comment: C: Responder Vs Non-Responders Paired Comparison DESEQ2
... I might be missunderstanding something. But I thought pennakiza was asking for the difference in gene expression between the group of responders (N=1 in this case) and the group of non-responders. But the interaction term given here would give the difference in treatment effect between responders an ...
written 8 months ago by brynedal0

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