User: mlai2567

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mlai25670
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Posts by mlai2567

<prev • 15 results • page 1 of 2 • next >
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Cytoscape Nodes/Interactions Export
... Hi All, Does anyone with Cytoscape experience know how I might be able to export my network data as a table of nodes and their respective interactions? I've tried exporting as an SIF but it doesn't seem to include the specific nodes and interactions. Thanks in advance! Cheers, Michael ...
network analysis cytoscape written 20 days ago by mlai25670 • updated 14 days ago by scooter80
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Comment: C: Differential Expression Help
... Thank you both for your responses! I understand that the experimental setup was not ideal given my limited resources, and will hopefully be able to perform additional replicates for each condition in the future. However, because I will not be able to sequence additional samples for some time I will ...
written 6 weeks ago by mlai25670
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Comment: C: Differential Expression Help
... That was an option I've been considering. However, when I do that, the analysis runs as if there was no replicate, which I wasn't sure was acceptable or not? ...
written 6 weeks ago by mlai25670
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Differential Expression Help
... Hi all, I'm trying to analyze an RNA-seq dataset that was just run. It consists of 3 conditions (Control, Treatment 1, Treatment 2) with 2 biological replicates (Cell line #1, Cell line #2) each. However, because the biological replicates are from cell lines of different passage number, there is ...
rna-seq differential expression edger written 6 weeks ago by mlai25670 • updated 6 weeks ago by Biostar ♦♦ 20
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Help with R differential expression analysis
... Hello All, I’m currently using the DE analysis App to analyze my RNA-sequencing data (https://yanli.shinyapps.io/DEApp/). However, I’m receiving the error “cannot coerce class ‘"try-error"’ to a data.frame” when inputting my data. Would someone be able to help me troubleshoot this issue? Thank ...
R rna-seq written 9 weeks ago by mlai25670
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RNA-seq Differential Gene Analysis
... Hi All, I'm currently performing differential gene analysis on my RNA-seq data set. What is the common threshold utilized for analysis in terms of fold change. I've currently set the fold change threshold at 1.5. Is this stringent enough? Thanks in advance! ...
rna-seq written 3 months ago by mlai25670
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GeneMANIA Network Creation
... Hello all, I am currently using the GeneMANIA Cytoscape plugin to create network interaction maps based off of my RNA-seq data. I am currently debating if I should include "Gene Interactions," defined by the GeneMANIA FAQ as "functionally associated if the effects of perturbing one gene were found ...
genemania rna-seq written 3 months ago by mlai25670
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Comment: C: Help with RNA-seq analysis
... From what I've gathered at this point, it seems to me that each platform performs essentially the same task using different statistical assumptions? On the basis that each method will probably produce slight variations in data, is it necessary to utilize all methods for analysis, and rationalize t ...
written 4 months ago by mlai25670
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Answer: A: Help with RNA-seq analysis
... I've come across the following web-based application which is fitting my purposes nicely: https://gallery.shinyapps.io/DEApp/ A question to you guys. What are the primary differences between edgeR, Limma-Voom, and DeSEQ? Is one more widely used than the others? For publication, would reviewers pre ...
written 4 months ago by mlai25670
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Comment: C: Help with RNA-seq analysis
... Thank you for the replies! I'm currently trying to use the Galaxy platform to perform my DESeq analysis. However, I am unsure of how to convert my Excel data-sheet into a suitable file for Galaxy analysis, and how to setup the correct parameters. Would someone kindly be able to guide me through this ...
written 4 months ago by mlai25670

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