User: lucap

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lucap0
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Posts by lucap

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Comment: C: ClusterProfiler GSEA with geneList
... Thanks Ludwig for the clear explanation! I see what you mean. I’ll carry the over-representation test then Thanks Luca ...
written 4 months ago by lucap0
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ClusterProfiler GSEA with geneList
... Hi everyone, Just a quick question. I want to perform GSEA on my geneList using clusterProfiler. Since I have a lot of genes and for some of them the logFC is small, I would like to perform GSEA only on the genes that have a logFC > 2. How do I do that in R? I am following the recommended steps ...
clusterprofiler gsea genelist written 4 months ago by lucap0 • updated 4 months ago by Ludwig Geistlinger50
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Comment: C: EdgeR glmTreat error
... Sorry for the three posts, I honestly don't know how I did it... Thanks for the detailed explanation, now I get what you mean about the `contrast`. So basically with `glmQLFTest` I will find all genes that are significantly differentially expressed (not up-reg or down-reg, just significantly DE) at ...
written 7 months ago by lucap0
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Comment: C: EdgeR glmTreat error
... Thanks James for your reply. I am sorry but I don't understand what you mean. According to this guide ([link][1]) the object `con` is a matrix... Plus, sorry, what do you mean with "it makes no sense in the context of an ANOVA-like test of multiple comparisons"? Thanks Luca [1]: https://www.g ...
written 7 months ago by lucap0
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EdgeR glmTreat error
... Hi all, I am using edgeR to identify genes differentially expressed in my experiment. I have cells which were grown in 4 different cell media and I would like to perform an ANOVA to identify DE genes comparing all media vs all (e.g. media1 vs media2; media1 vs media3; media1 vs media4; media2 vs med ...
edger error written 7 months ago by lucap0 • updated 7 months ago by James W. MacDonald51k

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