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To this end, we analyzed the entire ENCODE data set (780 ChIP-seq files) with the QuEST peak caller, using moderate identification criteria (chip enrichment = 30) (Valouev et al. 2008).
Poor quality samples were excluded from the study if they met the following criteria: chip call rate < 97%; log R ratio standard deviation > 0.27; B allele frequency standard deviation > 0.17; and PennCNV wave factor > 0.04 or ≤ 0.04 (Diskin et al. 2008).
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Assisted by the meshing criterion, chip-level simulators are capable to obtain the peak temperature of MMICs without using averaging approximations, and achieve considerably high simulation accuracy.
Data sets were selected based on the following three criteria: (1) chip platform (Affymetrix human genome U133 plus 2.0 expression arrays); (2) cell type studied; (3) availability of raw data (.cel) files.
Data sets were selected based on the following criteria: (1) chip platform (only data from Affymetrix Human Genome U133 Plus 2.0 expression arrays was included); (2) primary cell; (3) cell-subset studied; (4) availability of raw data (.cel) and sample description files.
Due to the second criterion 3 4 chips with extremely low RNA quality were excluded from the whole dataset.
These selection criteria suggested that CHIP would be a more selective antitumour agent than Neoplatin, and will provide a basis for its comparison with the other 7 compounds.
Importantly, also probe design and selection have been improved by applying more sophisticated genomic and thermodynamic criteria especially for chip generations following the U95.
This will affect sources that dither across multiple CCDs, where one or more of the CCDs are off or are otherwise excluded (see the "Observation Selection" page for a description of the criteria by which chips are excluded, as well as for the list of ObsIDs with dropped chips).
Lin and Huang [18] studied nano-cutting process by MD simulation and proposed the innovative 'combined Morse potential function and rigid tool space restrictions criterion' as the chip separation criterion.
Quality control was performed within-breed on the HD and 50K genotypes, using the same criteria for both chips.
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