User: ninabhatia3

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Posts by ninabhatia3

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Comment: C: WGCNA modules and categorical traits relationship
... Hi Kevin, How would you reccomend we build the logistic regression model. I am relatively new to R and having a lot of trouble trying to download nnet and follow this tutorial linked below for building a multinomial logistic regression model. https://www.youtube.com/watch?v=fDjKa7yWk1 ...
written 4 weeks ago by ninabhatia30
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Comment: C: WGCNA Module Trait Correlation
... No I'm not that user ...
written 5 weeks ago by ninabhatia30
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Comment: C: WGCNA Module Trait Correlation
... Hi, I am not sure I was clear. I am using am applying the code in the tutorial to my own data. Therefore I am changing the lines of code that delete part of the expression data and trait data since I am only trying to find the correlation between gene modules and one trait. Other than that I am not ...
written 5 weeks ago by ninabhatia30 • updated 4 weeks ago by RamRS23k
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WGCNA Module Trait Correlation
... I am trying to find the correlation between gene modules and the tissue where the gene was found in. I have 2 seperate CSV files. One containing the genes and the gene expression in each sample. The second CSV file contains a column of the sample identifier and a column of the tissue the sample was ...
software error written 6 weeks ago by ninabhatia30 • updated 6 weeks ago by Kevin Blighe46k
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Comment: C: WGCNA Different Module Results
... Thank you so much! Do you know why the Hovarth code uses this command : dynamicMods = cutreeDynamic(dendro = geneTree, distM = dissTOM, method="hybrid", deepSplit = 2, pamRespectsDendro = FALSE, minClusterSize = minModuleSize); when creating modules stepwise as opposed to this command used in th ...
written 7 weeks ago by ninabhatia30
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WGCNA Different Module Results
... I'm using WGCNA to find gene modules- I've been using both the code from http://pklab.med.harvard.edu/scw2014/WGCNA.html and from here https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ and I am getting different results in the number of modules/module sizes. Can a ...
R rna-seq written 7 weeks ago by ninabhatia30 • updated 7 weeks ago by Sam2.4k

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