User: Arvid Sondén

gravatar for Arvid Sondén
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5 years, 3 months ago
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5 years, 4 months ago
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Posts by Arvid Sondén

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limma, analysis on subset of data gives completely different results
... Dear all, I am currently working with gene expression analysis in limma. I have a total of 146 samples divided into 21 groups. What I want to do is pairwise comparisons between one group (the control group) and the others. The following code shows this for the first pairwise comparison between grou ...
limma written 5.3 years ago by Arvid Sondén40 • updated 5.2 years ago by Gordon Smyth38k
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Comment: C: p-values from robust linear model in LIMMA
... Dear Gordon, Thank you for your answer! My issue is that I want to use my p-values for filtering, but when using method="ls" (even if using robust=TRUE in eBayes) I get no significant values after adjusting for multiple testing at all. Using the robust method in lmFit however generates a distribut ...
written 5.4 years ago by Arvid Sondén40 • updated 4.8 years ago by Gordon Smyth38k
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p-values from robust linear model in LIMMA
... Dear all, I am currently working with expression data in LIMMA and have been asked to fit a robust linear model: lm.fit.rob <- lmFit(object=y$E,design=m.matrix, method="robust") lm.fit.rob.bayes <- eBayes(lm.fit.rob) lm.fit.rob.bayes.tt <- topTable(lm.fit.rob.bayes,coef="Group") It is e ...
limma lmfit written 5.4 years ago by Arvid Sondén40 • updated 4.8 years ago by Gordon Smyth38k

Latest awards to Arvid Sondén

Popular Question 5.3 years ago, created a question with more than 1,000 views. For limma, analysis on subset of data gives completely different results
Popular Question 5.3 years ago, created a question with more than 1,000 views. For p-values from robust linear model in LIMMA

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