User: brohawndg

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brohawndg50
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New User
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United States
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2 years, 2 months ago
Joined:
2 years, 9 months ago
Email:
b********@vcu.edu

Posts by brohawndg

<prev • 10 results • page 1 of 1 • next >
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Answer: A: WGCNA Hub Gene Selection Method
... Hello Dr. Langfelder,   Thanks for your response. We do have a number of interesting candidate genes with high kME values and high gene significance values within our module of interest. However, the ranking of these genes based on IM connectivity vs kME is similar, but not identical. To ensure I ...
written 2.4 years ago by brohawndg50
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WGCNA Hub Gene Selection Method
... Hello, I recently finished a WGCNA analysis with much success! We found a module whose eigengene is highly associated with disease status and whose GO results indicate the module genes are associated with inflammatory processes that have been recurrently associated with the disease previously. My ...
wgcna hub genes kme intramodular connectivity written 2.4 years ago by brohawndg50 • updated 2.3 years ago by Peter Langfelder1.3k
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Theoretical WGCNA Question
... Hello, I recently used WGCNA to analyze a 15 sample set (7 cases and 8 controls), and it appears to have worked swimmingly. The analysis yielded a resulting module highly correlated to disease status (.7) and the GO results are highly consistent with previous literature for this disease. Looking fo ...
wgcna theory scale-free topology written 2.7 years ago by brohawndg50 • updated 2.6 years ago by Peter Langfelder1.3k
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Answer: A: WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Hi Dr. Langfelder,   Have you had a chance to look over the error message I received when trying to use the maxPOutliers flag in the adjacency command?   I'm guessing my previous question got buried in the shuffle.   Thanks! Dave Brohawn ...
written 2.7 years ago by brohawndg50
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Answer: A: WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Hi Peter,   Thank you again for all of your help.   I was able to add corOptions=list(maxPOutliers=0.1) to the pickSoftThreshold command: sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5, networkType ="signed hybrid", corFnc= "bicor", corOptions=list(maxPOutliers=0.1))  and r ...
written 2.7 years ago by brohawndg50
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Answer: A: WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Hello,    I should add that I was able to apply the bicor function to my datExpr variable as below:   Test <- bicor(datExpr, use="pairwise.complete.obs", maxPOutliers=0.1)   prior to using the pickSoftThreshold command, though I am not sure if that was appropriate. Thanks again,   David ...
written 2.7 years ago by brohawndg50
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Answer: A: WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Hello Peter,    I have been practicing with the online WGCNA tutorials in preparation of running our analysis, and have a followup question regarding proper usage of bicor and maxPOutliers:   I successfully created the datExpr and datTraits variables as instructed in the data input and cleaning ...
written 2.7 years ago by brohawndg50
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Answer: A: WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Many thanks sir! Very excited to see what comes out. David Brohawn ...
written 2.8 years ago by brohawndg50
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Answer: A: WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Hello Peter, Thanks for your quick reply. I already filtered and log transformed my FPKM values, so they are ready to go.   If we run a standard WGCNA analysis with these 15 samples' pre-processed data using the bicor and maxPOutliers flags you recommended:   Could I then set disease/control s ...
written 2.8 years ago by brohawndg50
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WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Hello,   My name is David Brohawn and I am a 4th year graduate student at Virginia Commonwealth University.   My advisor and I research ALS (Lou Gherigs disease). I have recently generated high density (50 Million 2X150 read pairs) RNA-Sequencing data for 15 human postmortem spinal cord tissue h ...
wgcna sample size outliers written 2.8 years ago by brohawndg50 • updated 2.2 years ago by mh.manoj0

Latest awards to brohawndg

Great Question 2.2 years ago, created a question with more than 5,000 views. For WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Theoretical WGCNA Question
Popular Question 2.2 years ago, created a question with more than 1,000 views. For WGCNA Hub Gene Selection Method
Popular Question 2.2 years ago, created a question with more than 1,000 views. For WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation

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