User: Ahill
Ahill • 920
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Posts by Ahill
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... Downloading ref genome .fasta and checking ref strand will certainly work, and can be done quickly. C/G or A/T SNPs may be ambiguous. Checking your alleles against dbSNP may be an option (they maintain a VCF), I'm not aware of a batch lookup tool that would do that for you without at least some sc ...
written 5 weeks ago by
Ahill • 920
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Comment:
C: R - writeXstringSet
... Have you looked at ?DNAStringSet constructor help page? DNAStringSet() expects a character vector of strings or a Xstring object as a first argument, where you have 'df', a variable which does not appear to be initialized before first use. If you are seeking to generate .fasta files for a subset o ...
written 6 weeks ago by
Ahill • 920
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... 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 5 months ago by
Ahill • 920
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... 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 6 months ago by
Ahill • 920
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... 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 6 months ago by
Ahill • 920
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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 6 months ago by
Ahill • 920
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... 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 6 months ago by
Ahill • 920
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... 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 6 months ago by
Ahill • 920
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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 7 months ago by
Ahill • 920
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... 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 7 months ago by
Ahill • 920
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created a comment with at least 3 up-votes.
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