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The initial report (YPED version 1.0) [13] described analysis requisition, result reporting and sample comparison for multi-dimensional protein identification technology (MudPIT) [19], difference gel electrophoresis (DIGE) [20], and isotope-coded affinity tag (ICAT) labeled [21] samples.
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These files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals).
For physical examination, examination of growth was not included in the full and balanced sample comparisons for the same reason.
Thresholds were set, and the resulting BED files were analyzed using Genpathway IP (San Diego, CA, USA) analysis software, which provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals).
The sample comparison details for the identification of the DMR sets described in this study are described below.
Each gDNA sample comparison used for CGH was labeled using a NimbleGen Dual-Color DNA Labeling Kit.
A straightforward adaptation of the OD method would be to incorporate weights that would decrease the influence on sample-sample comparisons for a given gene if the samples themselves were highly dissimilar.
4 Population means were compared using the z-test for large sample comparison and t testing for comparison of results at each INR value.
A split sample comparison is conducted for estimating the values tourists give to a set of landscape attributes.
After screening for adequate SNR, signal intensity values were then used as the data for sample comparison.
For sample comparison, peptide intensities were derived from the summed intensity of the transitions.
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