User: alserg

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alserg260
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Posts by alserg

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Bonferroni multiple corrections question
... To clarify: fgsea adjusted P-values are Benjamini-Hochberg-adgjusted, not Bonferoni. ...
written 4 weeks ago by alserg260
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News: Bioinformatics Contest 2020. Call for problems
... This is a call for problems for the online Bioinformatics Contest 2020. We have been holding the Contest since 2017 ([https://bioinf.me/en/contest][1]), and we hope to make it more diverse and international in the upcoming years. An important step in that direction for us is to ask the bioinformati ...
news contest written 9 weeks ago by alserg260
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Answer: A: Getting all gene members in a Reactome Pathway
... There is a package `reactome.db`: http://bioconductor.org/packages/release/data/annotation/html/reactome.db.html There you can select genes from reactome pathways. However, the IDs are not consistent with the online version, although pathway names are consistent. ...
written 3 months ago by alserg260
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Answer: A: PCA on RNAseq time series data
... You can do a PCA plot in our tool Phantasus: https://genome.ifmo.ru/phantasus/ or https://artyomovlab.wustl.edu/phantasus/ Open your dataset (xlsx or txt file) with "Open your own file menu/My computer". Do Tool/Ajust, check "One plus log2" and "quantile normalization". Then Tools/Plots/PCA plot ...
written 3 months ago by alserg260
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Answer: A: Need help choosing genes and calculating ranks for GSEA rank file
... 1) I recommend to consider "all genes" as all expressed genes, considering only top 10-12K most expressed genes (by average expression, or baseMean, if it's a result of DESeq2). You can use all the genes as well, but the list will contain a lot of noise. As for 2) and 3) you can use stat field of t ...
written 4 months ago by alserg260
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Tool: Phanantasus: a web-application for exploratory gene expression analysis and visualization
... [Phantasus][1] is a web tool designed for visual and interactive gene expression analysis. In particular, it was designed to allow to go from a typical dataset to differential expression and downstream analysis in an easy and streamlined manner. For that aim, Phantasus integrates an intuitive heatma ...
geo microarray heatmap gene expression rna-seq tool written 4 months ago by alserg260
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Answer: A: Max/min value of enrichment score
... No, it's not possible. The maximal and minimal ES values are exactly 1 (when the selected genes are exactly the top up-regulated) and -1. You can check out the section "4.1 Geometric interpretation of GSEA statistic" of fgsea preprint (https://www.biorxiv.org/content/10.1101/060012v1.full) for the ...
written 4 months ago by alserg260
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Answer: A: Preranked GSEA statistics
... NES stands for normalized enrichment score. It's calculated as the enrichment score value of the pathway divided by the average enrichment score of random gene sets of the same size and the same ES sign. FDR corrseponds to p-value adjusted to multiple hypothesis comparison. Although, if you use th ...
written 5 months ago by alserg260
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Answer: A: GSEA on preranked list with weighted enrichment statistic (exponent=1) in R
... Could you clarify what exactly you can't reproduce? Both DOSE and ClusterProfiler use fgsea as a backend, so if it's possible with DOSE it should work fine for fgsea. ...
written 7 months ago by alserg260
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Comment: C: Pathway test for reversal of effect (three-condition comparison)
... I got `ranks = (m2 - m1) / (s1 + s2)` where `m2` and `m1` are means, and `s1` and `s2` are standard deviations for the corresponding samples. This better forces top genes to have small variance between AB and zero samples. Btw, I remembered it was used in a published paper, so it may be useful to c ...
written 15 months ago by alserg260

Latest awards to alserg

Scholar 20 months ago, created an answer that has been accepted. For A: Is there a name for these charts?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler

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