User: Collin

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Collin630
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630
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United States
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11 hours ago
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3 years, 2 months ago
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Posts by Collin

<prev • 71 results • page 1 of 8 • next >
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Comment: C: Effect size of a SNP - contribution to genetic variance
... Yes, one would need to add the variance of the epsilon term to get the full variance of Y, Var[Y] = Var[BX] + Var[epsilon]. But the variance of the random noise term wouldn't be considered a genetic influence on the phenotype. ...
written 8 days ago by Collin630
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Answer: A: Benjamini+ Hochberg multiple testing p.adjust R
... TL;DR There is nothing wrong with the output from the p.adjust function using the "BH" method. If you had more p-values that were not as highly similar, the results would generate different "adjusted p-values" from the "BH" method. You can see the exact calculations performed by p.adjust by simply t ...
written 6 months ago by Collin630
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Comment: C: Constructing a mean ROC curve based on 5 iterations
... Yes, I meant to concatenate them into a single vector. Nearly all methods provide a score which is used for ranking. It's odd that it's not provided as output. They may have an internal score that is just not getting returned to the user. You might need to contact the authors or see if you can modif ...
written 6 months ago by Collin630
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Answer: A: Constructing a mean ROC curve based on 5 iterations
... What happens in 5-fold cross-validation is that you train on 4 of the folds and predict on the hold-out fold. This procedure is repeated until all folds have hold-out predictions on them. Given this preamble, you could just concatenate the scores and labels from the 5 hold-out predictions (which sho ...
written 6 months ago by Collin630
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Comment: C: Computing ROC curves without scores
... the Precision-Recall curve basically assesses what your saying. Precision is the fraction of predicted positives that are labeled as true positive (also known as positive predictive value). You can always mark with a dot the precise point on the curve that equals the top 100 genes. This would give y ...
written 7 months ago by Collin630
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Comment: C: Computing ROC curves without scores
... I disagree on the point that ROC curves doesn't give the following information "how many genes you need to take to get a given sensitivity value". You can in fact pick the corresponding number of genes from the threshold that produces X% sensitivity on the ROC curve (and understand what the false po ...
written 7 months ago by Collin630
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Comment: C: Computing ROC curves without scores
... Yep it is a network-based gene prioritization approach. Based on their paper, it does create a score that it uses to rank the genes. However, from their user documents they don't provide it as an output. So from a practical perspective, like Jean-Karim noted, you likely have to use the rank of the g ...
written 7 months ago by Collin630
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Comment: C: Computing ROC curves without scores
... That's odd that the program doesn't give you a numerical value. Without a numerical value you have no way of knowing whether two genes were tied on a prioritization assessment. So you likely will have to just assume no ties. I think the most explainable way is what you propose, that is you construct ...
written 7 months ago by Collin630
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Comment: C: Alternative tools replace MutDB to predict consequences of deleterious SNV
... Could you clarify whether you are interested in germline mutations or somatic mutations? The table you include has many cancer-specific methods, but the semantic "deleterious SNV" would suggest you are interested in germline mutations. ...
written 11 months ago by Collin630
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Answer: A: Alternative tools replace MutDB to predict consequences of deleterious SNV
... You could use scores from the VEST algorithm (PMID: 23819870). It's pretty easy to score SNVs by just submitting them to the CRAVAT webserver (http://www.cravat.us/CRAVAT/, PMID: 29092935). In one of the latest papers to benchmark performance, VEST is among the best (PMID: 29179779). ...
written 11 months ago by Collin630

Latest awards to Collin

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 10 months ago, created a question with more than 1,000 views. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Supporter 11 months ago, voted at least 25 times.
Appreciated 16 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 2.2 years ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 2.8 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 2.8 years ago, asked a question with at least 3 up-votes. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Scholar 2.9 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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