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The testing plan will generate data on both platforms, using the same primer sets.
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Both platforms used the original OSEM algorithm [6], with 10 iterations and 10 subsets (for 120 projections) or 8 iterations and 12 subsets (for 128 projections).
Although this evaluation was based on the Human Methylation27 platform, we expect these principles should be applicable to the new release of the 450 k Infinium Methylation Beadchip as both platforms use the similar Infinium methylation assay.
Thus, when the expression levels of the genes, identified by both array platforms using the vRNA depletion method (n = 25), were compared to the expression levels in the experiments without vRNA depletion, a significant increase in the fold changes was observed on both array platforms (Fig. 5B).
The sample typed as HLA-DRB1∗07:01 01 homozygous on both platforms using either the Twin or TypeSteam software analysis packages.
The microarray testing phases are designed to evaluate the candidate external RNA controls on both one-color and two-color platforms using the same pools of transcripts.
We matched the subjects and the markers that were common between both platforms using manual python and R scripts.
Using only the data of genes represented on both microarray platforms (n = 1,271), we applied a methodology evaluated by Warnat et al. [ 11], namely the median rank scores (MRS), to derive numerically comparable quantities from the expression values of both platforms used in the different studies.
Both platforms use basically the same process — differences are very minor and noted below: Tagging Photos: Go to the photo you want to tag.
Both platforms use inkjet-printed 60 mer oligonucleotide probes [ 46].
Expression values were used as features for the first classifier, either considering all genes present on both microarray platforms used, or the top 500 differentially expressed genes (available in Additional file 2).
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