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High-density assays, such as the BovineSNP50, have previously been shown to be adequate for the identification of runs of homozygosity (ROH) and for estimating inbreeding coefficients within cattle breeds [ 95].
To enhance the identification of runs of probes that detect STAT1 binding, probe intensities were smoothed by taking the mean intensites across a window of 20 probes (720 bp).
To enhance the identification of runs of probes that detect the presence of polyA RNA, we smoothed probe intensity values by taking the mean intensity across a window of 20 probes (400 bp).
To enhance the identification of runs of probes that detect RNApolII binding, probe intensities were smoothed by taking the mean intensites across a window of 20 probes (760 bp).
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Some of these salmon subpopulations are listed as endangered (winter run) or threatened (spring run), thus there has been active interest to develop reliable methods for identification of run among sampled fish.
Statistical variation of these parameters allows rational comparison of experimental runs and identification of outlier runs.
Comparison with current method (run-by-run correlation) demonstrates a significantly better rate of identification of outlier runs by the multivariate strategy.
To summarize, our method aims at the identification of poor runs among a group of LC-MS experiments.
The identification of fall run with unprecedented accuracy was demonstrated.
Results: We describe a novel multivariate statistical strategy for the identification of LC-MS runs with extreme peptide abundance distributions.
Without proper identification of statistical outlier runs the estimates of variance will be inflated, which may have a considerable effect on the identification of significant peptides and proteins.
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