User: eric.kern13

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eric.kern1370
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3 months, 1 week ago
Joined:
1 year, 5 months ago
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Posts by eric.kern13

<prev • 27 results • page 1 of 3 • next >
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Comment: C: cell surface receptor genes
... Thanks for this list of resources! ...
written 3 months ago by eric.kern1370
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Answer: A: Interpreting ANNOVAR allele frequency output
... Below, I quote a response from Kai Wang, ANNOVAR creator/maintainer: > you should just use table_annovar.pl to print out allele frequency for > all variants in your input. The word "minor allele frequency" cannot > be defined well, because rare allele in one population will be common > ...
written 3 months ago by eric.kern1370
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Interpreting ANNOVAR allele frequency output
... Hi Biostars, I'm using ANNOVAR to annotate some WGS data. I want to pare down the list until I am left with variants of very low frequency. I've got ANNOVAR working, but I'd appreciate your help interpreting its output. Here's what I did. To split out the rare variants, I issued this command (or r ...
genome sequencing written 3 months ago by eric.kern1370
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Comment: C: EdgeR or Ttest/ANOVA for non normal RNAseq data?
... How many rows of data do you have? Linear models such as ANOVA rely heavily on independence of errors and constant variability, but with enough data, normality is not as crucial. ...
written 9 months ago by eric.kern1370
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Comment: C: Can someone help me with imputation of missing SNPs using beagle 4?
... Did you check the locus it mentions ( 5:35101444 ) to see if there's anything wrong in the data? ...
written 9 months ago by eric.kern1370
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Answer: A: Comparing results from ADMIXTURE and EIGENSTRAT
... First, a couple of things that may have gone wrong: - There is no natural association between the first eigenvector and the first person, the second eigenvector and the second person, etc.  - Why does that comment say eigvals if you're talking about the individuals' eigenvectors? Now my answer. In ...
written 15 months ago by eric.kern1370
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Comment: C: Should I use the p-value or q-value for pathway analysis in DAVID?
... Suppose you accept a given case as "significant." You also accept everything with a lower p-value. The q-value of the case you accepted is the false discovery rate you should expect, i.e. E[ false positives / all positives]. ...
written 16 months ago by eric.kern1370
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Answer: A: Statistically significant overlap between three ranked lists
... It seems like you may be interested in a consensus ranking. Methods like this might help: http://www.jmlr.org/papers/volume11/meila10a/meila10a.pdf Unfortunately, I cannot find a software page or github account for the authors where the method might be available. ...
written 16 months ago by eric.kern1370
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Comment: C: Mappability Scores from bigWigAverageOverBed all zero
... This is the second time I've had this problem, and it makes me want to chrY. ...
written 17 months ago by eric.kern1370
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Answer: A: Mappability Scores from bigWigAverageOverBed all zero
... I solved this issue by switching to the bigWigSummary tool and writing 'chr22' in place of '22'.  ...
written 17 months ago by eric.kern1370

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Scholar 3 months ago, created an answer that has been accepted. For A: Looking for experience
Scholar 17 months ago, created an answer that has been accepted. For A: Looking for experience
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Looking for experience

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