User: joelrome88

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joelrome880
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Posts by joelrome88

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Comment: C: limma interaction contrasts
... Yes thank you! it's getting clearer now. If doing c(0,0,1,1) removes both interaction and treatment effect leaving just the effect of treatment in the mutants, would c(0,1,1,1) ask for any change due to either genotype OR treatment? Thank you so much for answering my questions! ...
written 2.4 years ago by joelrome880
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Comment: C: limma interaction contrasts
... Hi again, I tried using treat and topTreat but I didn't get different results. I have a naive question if a different paramterization answers the same questions. If using an intercept, and thus the contrasts as vectors of 0 and 1 I've come across different results. > design = model.matrix(~Gen ...
written 2.4 years ago by joelrome880
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Comment: C: limma interaction contrasts
... I see, I'll take a look at the decideTests - treat parameter. In the case of the third contrast (mut1B - wtA), is this a fair comparison to make by itself? In the case of an interaction effect, does this mean that the difference between the mean values of (wtB-wtA) and (mutB-mutA) is different fo ...
written 2.4 years ago by joelrome880
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limma interaction contrasts
... Hi, I have a quick doubt about my design matrix and if the contrasts I'm making are correct. I have an experimental design with two factors, genotype and treatment. I have 13 genotypes (control and 12 mutants) and two treatments (A being control and B the actual treatment). The groups made are the ...
limma limma design matrix limma contrast matrix written 2.5 years ago by joelrome880 • updated 2.5 years ago by Aaron Lun24k
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Comment: C: Effect of treatment vs control over time in RNA Seq (edgeR and limma)
... Hi Ryan,  If I understand correctly this is the same as doing:  > model.matrix(~0 + Time:Treatment + Strip, data=targets). Does it affect taking away the effects of time and treatment? I tried the model I jus wrote using an anova of contrasts:   > con <- makeContrasts('tm1'=Grouptm1.b - ...
written 3.2 years ago by joelrome880
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Effect of treatment vs control over time in RNA Seq (edgeR and limma)
... Hi everyone! This is a bit long but I hope to state my problem more clearly I've been trying to perform an analysis on the effects of a treatment over different time points using RNASeq with both limma and edgeR but I'm a bit confused with how to approach and interpret the results. The experiment ...
rnaseq limma edger voom multiple time points written 3.2 years ago by joelrome880 • updated 3.2 years ago by Ryan C. Thompson7.4k
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no DGE with multiple groups in edge R
... Good morning, I've been having an issue trying to look for DGE in edgeR. My main problem is that the FDR of ALL genes is 1. I have data for 5 timepoints, and two different conditions for each one (Control and treatment). Additionally, there is a starting point sample (time 0, no treatment). This m ...
rnaseq edger differential gene expression written 3.6 years ago by joelrome880 • updated 3.6 years ago by Aaron Lun24k

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For limma interaction contrasts

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