User: loicborcard01

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Posts by loicborcard01

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GSVA with a genesets as a list?
... Hello, I am trying to run GSVA with a list of genesets (because I couldnt make it to work with a genecollection object) , but it only uses the first geneset of the list for some reason. So I used a lapply to get it to calculate the enrichment score but the problem is that it doesn't output a formal ...
enrichment gsva written 3 months ago by loicborcard0110
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Comment: C: Where to find annotation infos for my Expressionset?
... Now that you saw how I created my expressionset you think you could help me? ...
written 3 months ago by loicborcard0110
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How to fix the error "Error in fastmatch::fmatch(x, y) : ..." ?
... Hello everyone, I am running GSVA on an expressionset and it is giving this error, I have been looking for a way to fix it but I did not find anything. Does anybody know what's causing this and how I could fix it? No annotation package name available in the input 'ExpressionSet' object 'expr'. ...
enrichment gsva rna-seq R written 3 months ago by loicborcard0110
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Comment: C: Where to find annotation infos for my Expressionset?
... Thank you, I am trying to use it properly but it turned out red idk why. ...
written 3 months ago by loicborcard0110
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Comment: A: Where to find annotation infos for my Expressionset?
... head(sampleinfos_day3) day animalid treatment 1 Day 3 G14 MOCK 2 Day 3 G15 MOCK 3 Day 3 G16 MOCK 4 Day 3 G17 MOCK 5 Day 3 G18 MOCK 6 Day 3 G19 MOCK dim(sampleinfos_day3) [1] 24 3 head(eset_matr ...
written 3 months ago by loicborcard0110 • updated 3 months ago by h.mon31k
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Where to find annotation infos for my Expressionset?
... Hello, I am running gsva on an ExpressionSet and a Geneset.collection that I created myself. And I get the error message written in red down below. I don't understand what's missing. `> eset ExpressionSet (storageMode: lockedEnvironment) assayData: 25880 features, 24 samples ...
R gsva rna-seq written 3 months ago by loicborcard0110 • updated 8 weeks ago by Biostar ♦♦ 20
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Comment: C: GSVA Enrichment score and correlation
... My question is: is it legitimate to do a ratio between the 2 ES and loose the sign (+/-) of my ES in the porcess and then use this value to calculate a pearson correlation ? On top of that the distribution of the ES score looks weird after this opperation. And second question would be: is there any ...
written 3 months ago by loicborcard0110
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GSVA Enrichment score and correlation
... Hi, I am working on a RNAseq dataset and I was asked to calculate the enrichment score(ES) (GSVA) of a cohort of 24 samples separated in 4 groups over 3 different days (day0,day3,day7). The next step is to correlate these scores with later (day10-Day63) readouts ( cellular responses, humoral repons ...
R gsva rna-seq written 3 months ago by loicborcard0110

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