Moderator: karl.stamm

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karl.stamm3.5k
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Posts by karl.stamm

<prev • 460 results • page 1 of 46 • next >
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Comment: C: Why do so many biomarker based classifiers claim high accuracy but rarely used i
... Good points. Let's add points 5) apriori probability. If your system detects something with a 99% accuracy (1% FPR) and the general population carries the disease at <= 2%, then your new test is no better than blind chance! 6) no practical workflow. I've seen new techniques touted that detect ...
written 3 days ago by karl.stamm3.5k
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Answer: A: Best statistical test for genotype-specific gene expression analysis
... I would do a linear trend, summary(glm()) does ANOVA for the correlation. Envision a scatter plot, x is the number of G's, 0,1,2. y is your log(expression). Statistical power is your problem, if you're looking at lots of genes or lots of SNPs, you will have false-positive results somewhere. If yo ...
written 7 weeks ago by karl.stamm3.5k
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Comment: C: Shannon vs Simpson for TCR diversity estimation
... What are you trying to achieve when you say evaluate TCR status? If you're worried about technical errors, try technical replication. See what the error rates look like. ...
written 7 weeks ago by karl.stamm3.5k
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Comment: C: RNAseq: What's the accurate way to test whether a set of N genes is differential
... The sequencing depth may vary between groups, so plain read-counts are misleading. If your control had better RNA handling, because they were processed before lunch, it may have more reads overall, and then all genes appear downregulated. Tools made for differential expression know this and accoun ...
written 9 weeks ago by karl.stamm3.5k
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Comment: C: RNA-seq: Is it worth to analyze case vs control separately to have a % similarit
... And the experimental design. Do we care about differences in Ca1 and Ca2? By the design of the experiment those differences should be considered background noise. ...
written 12 weeks ago by karl.stamm3.5k
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Answer: A: bash, how can I distinguish synonymous from non-synonymous variants in VCF files
... That kind of information is calculated based on the genomic reference and the gene's coding frame. There may be some transcripts of the gene that do not include Exon2, for example, for which the variant would be intronic. In another transcription frame, the same variant may be a stop-gain. In a ta ...
written 3 months ago by karl.stamm3.5k
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Answer: A: Diploid calls on chrY?
... Some regions of chrY are duplicated on chrX, it's called the pseudo-autosomal region, because it appears to behave like autosomes. Wikipedia tells me that this location, 59megabases could be included . https://en.wikipedia.org/wiki/Pseudoautosomal_region ...
written 4 months ago by karl.stamm3.5k
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Comment: C: Diploid calls on chrY?
... Big chunks of Y are copied on X, so maybe this is the so-called pseudo-autosomal region? ...
written 4 months ago by karl.stamm3.5k
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Comment: C: Missing data in covariate file in PLINK
... I don't know what your .bim is, but you should be able to recode any file, or just run the software separately for each condition. I gather PLINK is just running one column of the phenotype file anyway, you'll be doing separate analyses. You're trying to do several analyses right now with incompat ...
written 4 months ago by karl.stamm3.5k
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Answer: A: Missing data in covariate file in PLINK
... PLINK v1.9 has a parameter --missing-phenotype which lets you assign a number other than -9 as the key for missing value. see their docs for encoding parameters https://www.cog-genomics.org/plink/1.9/input#pheno ...
written 5 months ago by karl.stamm3.5k

Latest awards to karl.stamm

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Popular Question 15 months ago, created a question with more than 1,000 views. For Can I run VEP on a VCF twice?
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
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Teacher 23 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
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Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
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Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 3.2 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Appreciated 3.2 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
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