User: mikhael.manurung

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Posts by mikhael.manurung

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Comment: C: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
... I did not elaborate on that for the sake of brevity, but then apparently clarity was sacrificed. I fit an lmFit object named fit with the contrasts as below. fit.c <- contrasts.fit(fit, contrasts= contrast) fit2 <- eBayes(fit.c, robust=TRUE) To get the summary of DE genes in all contrasts, I ...
written 7 weeks ago by mikhael.manurung10
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Comment: C: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
... Thank you for your elaborate reply, Aaron. The point that I wanted to make (or confirm) for the first question is that topTable will control for FDR by treating the p-values as a single vector of values, just like supplying method=separate in decideTests to adjust for FDR separately for each tested ...
written 7 weeks ago by mikhael.manurung10
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Comment: C: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
... Dear Prof. Smyth, Suppose that I want to test the following null hypotheses: there are no differences between time points (t0, t1, t2) in group A, and there are no significant differences in pairwise comparisons of time points (see the contrast as defined below). I find single-factor design easier ...
written 7 weeks ago by mikhael.manurung10
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Comment: C: extracting the genes associated with the groups or samples in pheatmap.
... Hello Morteza, You said in your question that you have determined the genes that are significant. Which package did you use to determine that? If you use limma, then its user guide will surely benefit you. However, I get the feeling that what you have got so far is only the expression matrix. ...
written 7 weeks ago by mikhael.manurung10
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Comment: C: Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
... Speaking of F-test, I actually asked another question in this forum: question in this forum. Briefly, would the above command yield the same result as using decideTests with "method = nestedF" argument? ...
written 7 weeks ago by mikhael.manurung10
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nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
... Dear all, I would like to extend the discussion on my previous question regarding the contrast matrix. Briefly, I have data from two groups that are followed longitudinally at three different time points. After going through the workflow of the limma package, (lmFit, contrast fit, and eBayes), now ...
limma anova decidetests written 7 weeks ago by mikhael.manurung10 • updated 7 weeks ago by Gordon Smyth35k
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Comment: C: Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
... I really appreciate your responses! If you don't mind, I would like to further test my understanding of the contrast matrix. Suppose that I want to do an Anova-like tests for all time points of observation for group A (i.e. overall DEGs for group A). Then, is it correct if I design my contrast as su ...
written 7 weeks ago by mikhael.manurung10
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Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
... Dear all, I need your advice in designing contrast and design matrices for use in limma. My study consists of 2 groups that are followed longitudinally at three time points (repeated measures): Group has 2 factors, i.e. groupA and groupB. Timepoint has 3 factors, i.e. t0, t1, and t2. After b ...
limma design and contrast matrix design matrix contrast matrix written 7 weeks ago by mikhael.manurung10 • updated 7 weeks ago by James W. MacDonald48k
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Comment: C: Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
... Dear Ryan, Thank you for your response. Indeed, I did not have that many samples. I have to say that I really like the underlying principle of eBayes! Best, Mikhael ...
written 8 weeks ago by mikhael.manurung10
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Comment: C: Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
... Dear Prof. Smyth, Thank you very much for your response. I am also biased toward limma due to its ease of use and seamless integration with various downstream analyses. However, due to my lack of credentials as a bioinformatician, no one took me seriously when I (tried to) explain the eBayes princ ...
written 8 weeks ago by mikhael.manurung10

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