User: rhasanvandj

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Posts by rhasanvandj

<prev • 6 results • page 1 of 1 • next >
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heatmap in R
... Hello friends I want to make a heatmap for gene data in R. this is the code: geneExp <- read.table("file.txt", header=T, sep="\t") head(geneExp) # Extract just the numeric data into a matrix with named rows by gene rownames(geneExp) <- geneExp$Ge ...
gene written 2 days ago by rhasanvandj0 • updated 2 days ago by genomax85k
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GSEA for genes in R
... Hello, Is there any R code or tutorial to do GSEA in R for the genes and not pathways? Thanks ...
gsea for genes written 14 days ago by rhasanvandj0
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Comment: A: what is the cut-off for saying hat a gene set is positively/negatively represent
... Weird result mean no significantly enriched based on FDR <0.25. How should the gene IDs be similar? different programs accept different IDs format. ...
written 14 days ago by rhasanvandj0
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Comment: C: what is the cut-off for saying hat a gene set is positively/negatively represent
... Thanks GSEA only accept alphabetical IDs for genes ( i.e MUC16) and IPA for pathway analysis accept numerical values (i.e.94025 ). Differential gene expression can be done with mixed IDs (i.e. MUC16|94025) I dont think this can be the reason for weird result. what is your idea? ...
written 14 days ago by rhasanvandj0
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Comment: A: what is the cut-off for saying hat a gene set is positively/negatively represent
... Hi Kevin Thanks for responding. I dont know excatly what to tell yu. I am using hallmark in GSEA. What do you mean by code? I am running GSEA in server for broad institute. input is gct file and cls file for 2 phenotypes (patients having feature=1 and no feature=0) in the output no gene set is sign ...
written 15 days ago by rhasanvandj0
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what is the cut-off for saying hat a gene set is positively/negatively represented in GSEA?
... what is the cut-off for saying hat a gene set is positively/negatively represented in GSEA? I have 2 phenotypes and I have done GSEA. Based on FDR <0.25 no gene sets are significantly represented in the GSEA output. Why is that? Is FDR<0.25 the correct cut-off for GSEA? I have a large gene da ...
software error rna-seq written 15 days ago by rhasanvandj0

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