User: guillaume.rbt

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guillaume.rbt730
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Posts by guillaume.rbt

<prev • 207 results • page 1 of 21 • next >
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Comment: C: KEGG pathway enrichment analysis for wheat and barley
... I don't know how to do a KEGG pathway enrichment. But I know you could do GO enrichment analysis on with agrigo (http://systemsbiology.cau.edu.cn/agriGOv2/index.php) ...
written 1 day ago by guillaume.rbt730
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Ok great, I will definitely test it ! ...
written 1 day ago by guillaume.rbt730
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Ok thank for the tip ! (both markers are indeed also up-regulated :) ) ...
written 1 day ago by guillaume.rbt730
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Hi Eric and thank for your advices. I have in this case a high number of samples (111). I encountered similar results with what you described in your poster (better results with Limma/voom than with DEseq2 or EdgeR) ...
written 1 day ago by guillaume.rbt730
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Thank for your questions. The samples are collected before treatment, so the treatment has no effect on the profiles. I try to detect biomarkers that are predictive of a good response. The treatment tested is anti-PD1 checkpoint inhibitors, and it is expected to have a higher immune response activi ...
written 1 day ago by guillaume.rbt730
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RNAseq differential expression analysis : relevance of Immunoglobulin genes enrichment ?
... Hi all, I'm currently studying RNAseq samples, obtained from human tumor biopsies before treatment (111 samples). I'm comparing responders and non responders to the treatment, with the aim of identifying response biomarkers. In my results, I detect a strong enrichment for up-regulation of Immunog ...
immunology rna-seq written 2 days ago by guillaume.rbt730
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Answer: A: How to plot GSEA result?
... If you are using the GUI version of GSEA you can set the number of plots that will be generated. You have to go in "advanced fields" where there is a field "Plot graphs for the top sets of each phenotype" which sets the number of plots. ...
written 2 days ago by guillaume.rbt730
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Answer: A: too few differentially expressed genes with large number of replicates, using ea
... When I encounter this kind of situation I like to do some "sanity checks". Maybe you could add artificial controls genes in your expression data to try to understand how the tools are behaving, the best is to do add like 10 genes with a scale of expression difference, from the same expression betwe ...
written 6 days ago by guillaume.rbt730
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Comment: C: Scatter plot for GSEA results analysis
... I don't understand what the "number of significant genes" corresponds to in the GSEA results. Is it the number of genes marked as "core enrichment"? ...
written 8 days ago by guillaume.rbt730
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relevance of GSEA on Nanostring ncounter gene expression data ?
... Hi all, I'm currently doing analysis on a gene expression dataset produced with the nanostring ncounter method, on a panel of around 700 genes (all involved in the immune system) I want to test for gene set enrichment, based on the differential expression analysis I've performed between two condit ...
nanostring gsea written 12 days ago by guillaume.rbt730 • updated 12 days ago by i.sudbery6.3k

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