User: Ahill

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Ahill900
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900
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5 years, 6 months ago
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Posts by Ahill

<prev • 81 results • page 1 of 9 • next >
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Comment: C: positive control and negative control genes list
... Or [GEO][1], [Expression Atlas][2]? [1]: https://www.ncbi.nlm.nih.gov/gds?term=breast%20estrogen%20positive&cmd=correctspelling [2]: https://www.ebi.ac.uk/gxa/query?geneQuery=%5B%5D&organism=homo%20sapiens&conditionQuery=%5B%7B%22value%22%3A%22breast%20cancer%20cell%20line%22%7D%5D ...
written 7 weeks ago by Ahill900
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Comment: C: Can microarray and RNA Seq. values from the same dataset be numerically compated
... What type of microarray and normalization methods? For oligo microarrays (e.g. Affymetrix) - generally no. Hybridization intensities can be probe-sequence dependent, so if Gene A has an intensity of 10 and Gene B has intensity 20, it would be very risky to to conclude B is expressed at twice the l ...
written 9 weeks ago by Ahill900
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Answer: A: Why gene expression data should be log2 transformed?
... When it is used, a main rationale for log-transformation is heteroskedasticity. The variance of expression measurements on many platforms (arrays, etc.) depends on the expression level. By log-transforming, you reduce this dependence and your data becomes better-behaved for statistical testing. A ...
written 9 weeks ago by Ahill900
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Comment: C: miRNA-Gene Interaction P-Values
... Apparently no. The authors say "[the pCT] reflected the Bayesian estimate of the probability that a site is conserved due to selective maintenance of miRNA targeting rather than by chance or any other reason not pertinent to miRNA targeting". So this is definitely not a type I error measure like a ...
written 10 weeks ago by Ahill900
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Answer: A: miRNA-Gene Interaction P-Values
... TargetScan provides a database of miRNA-gene interactions including a pCT statistic for the interactions. For human, downloadable from here: http://www.targetscan.org/cgi-bin/targetscan/data_download.vert71.cgi ...
written 10 weeks ago by Ahill900
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Answer: A: Understanding standardized genotype matrix
... Not a geneticist, but using your notation, for autosomes 2p is the expected (mean) value of x and sqroot(2p(1-p)) will be the standard deviation of x. So this is a [z-score][1]. The standardized values (wij) will have mean zero and variance 1 for each SNP, I guess a nice property for some calculat ...
written 11 weeks ago by Ahill900
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Answer: A: SNPRelate data file
... Instructions to create a GDS file: http://corearray.sourceforge.net/tutorials/SNPRelate/#create-a-gds-file-of-your-own ...
written 3 months ago by Ahill900
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Comment: C: Normalisation of arrays with global changes expected
... Just speculating, but two approaches to select a control gene set would be selection of "known" housekeeping genes (e.g. GAPDH, Actin, etc.), or rank invariant set normalization to select genes whose ranks are stable across samples (original ref I believe at https://www.ncbi.nlm.nih.gov/pmc/articles ...
written 3 months ago by Ahill900
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Comment: C: Getting Risk Allele from GWAS Odds Ratio?
... Interested in responses on this. I'd think fundamentally there is no way to reliably infer risk allele given only p/odds ratio for a SNP. I think it's a common, but not certainly not universal, convention that the minor allele is used as effect allele in common software used to compute association ...
written 4 months ago by Ahill900
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Comment: C: Intersection of flow cytometry and bioinformatics
... In immunophenotyping, some common goals are to either quantify the number of cells in previously defined cell populations, or to identify new, previously unknown groups of cells that correlate with a response of interest. In both those cases, "bioinformatics" approaches for supervised and unsupervi ...
written 5 months ago by Ahill900

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