User: Regeroka

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Regeroka0
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Posts by Regeroka

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FDR and mixed FDR in limma fry()
... Hi, I'm analyzing a large number of gene sets in RNAseq data, hoping to find sets that can differentiate between 2 conditions. I'm using `fry()`, from the limma package. I understand that there are 3 different hypotheses tested for each gene set (upregulated, downregulated, and the last one to my ...
limma fdr written 4 months ago by Regeroka0 • updated 4 months ago by Gordon Smyth38k
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Comment: C: How does normalisation affect the outcome of the Limma t-test like test (using t
... Alright, thank you very much! ...
written 4 months ago by Regeroka0
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Comment: C: How does normalisation affect the outcome of the Limma t-test like test (using t
... Sorry, my previous comment was not the best put. What I meant with (or rather instead of) using pathways, is that the genes (whose expression is to be averaged) are co-expressed, or we have a reason to believe so. So you would end up with a matrix of gene signatures (e.g. for pathways, or biological ...
written 4 months ago by Regeroka0
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Comment: C: How does normalisation affect the outcome of the Limma t-test like test (using t
... Thank you for your answer! How about using gene signatures? (e.g. taking all genes related to a certain pathway, and average their expression, and then repeat for multiple pathways. For that, the expression has to be scaled, so the individual genes are comparable.) Would this also cause an issue? ...
written 4 months ago by Regeroka0
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How does normalisation affect the outcome of the Limma t-test like test (using the eBayes() function)?
... Hi all, I am using the limma t-test on RNA-seq data, to compare the expression profiles between 2 conditions. I get different results when using log-expression values to when I'm using (z-score) normalised log-expression values. Do you know why that could be, how scaling could affect a t-test? S ...
limma written 4 months ago by Regeroka0 • updated 4 months ago by Gordon Smyth38k

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