User: egeulgen

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egeulgen600
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Posts by egeulgen

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... In some cases (especially if the number of input genes is low), pathfindR may not find any active subnetworks and therefore no enriched pathways. The message stating "Could not find any interactions for XX (XX%) genes in the PIN." is more relevant for genes not mapping onto the PIN. ...
written 5 weeks ago by egeulgen600
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Yes you should use your own expression data. **This is the data you used to perform differential expression analysis** and obtain the logFC and p values. pathfindR does not (cannot) create the expression data as it only uses the logFC values provided for enrichment. The expression matrix (input of l ...
written 5 weeks ago by egeulgen600
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hey, The expression matrix is the matrix you used to perform the differential expression test. Something like: GSM389703 GSM389704 GSM389705 FAM110A 9.8591 10.529 11.3828 RNASE2 10.3410 10.400 9.1157 S100A8 14.9554 15.012 12.9907 For the example da ...
written 5 weeks ago by egeulgen600
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Comment: C: Allele frequency comparison by Fisher's exact test
... I provided the example R code in my response (see above). There N_SNP is replaced with 3000 and for fisher.test you have to do something like: fisher.test(table(my_genotypes[i, ], 1kg_genotypes[i, ])) This does depend on how you store the two. ...
written 6 weeks ago by egeulgen600
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Answer: A: Allele frequency comparison by Fisher's exact test
... You may perform multiple Fisher's exact test, store the p values and then adjust them. In R, you would do something along the lines of: ### Perform Fisher's exact and store the p-values p_vals <- c() for (i in 1:N_SNPS) { result <- fisher.test(...) p_vals <- c( ...
written 6 weeks ago by egeulgen600
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Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... The expression matrix for the pathway scores is the same matrix as the one you use for differential expression analysis. Columns are samples, rows are genes and the values are expression values. ...
written 4 months ago by egeulgen600
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Comment: C: Plotting the expression values for two genes in a range of cells
... you have to have a column called `Cell` filled with the row names, i.e. `"cell1, cell2, ..."` should be in a column named `Cell` ...
written 5 months ago by egeulgen600
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Answer: A: Plotting the expression values for two genes in a range of cells
... You can plot such a "lollipop plot" using ggplot2: cell_data <- read.csv("~/Downloads/data.csv") library(reshape2) library(ggplot2) cell_data_molten <- melt(cell_data) cell_data$Total <- cell_data$Gene.A + cell_data$Gene.B for_levels <- cell_data$C ...
written 5 months ago by egeulgen600
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Comment: C: Gene expression meta analysis
... see this [related question][1] [1]: https://www.biostars.org/p/207056/ ...
written 5 months ago by egeulgen600
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Comment: C: Building a biologically meaningful design matrix for limma/voom in a large RNASe
... Since the mutations are mutually-exclusive I'd create a vector `Muts`, in which the mutation status is specified for each subject, i.e.: Muts <- c("Mut1", "Mut1", "Mut2", .... , "Control", ...) I would create a design matrix as below: Mutations <- factor(Muts, levels = c("Mut1", "Mu ...
written 5 months ago by egeulgen600

Latest awards to egeulgen

Popular Question 19 days ago, created a question with more than 1,000 views. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Librarian 9 weeks ago, created a post with more than 10 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Prophet 4 months ago, created a post with more than 20 followers. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Appreciated 5 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR
Scholar 5 months ago, created an answer that has been accepted. For A: Plotting the expression values for two genes in a range of cells
Appreciated 5 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Appreciated 7 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: enrichment of gene set with enrichR
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR

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