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All samplings were performed in two biological replicates producing a total of 52 leaves and 52 root samples.
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We demonstrated that three biological replicates produced a substantial improvement in fold-change detection over two; we recommend using at least three biological replicates if possible.
The average FPKM and RPKM values between the two biological replicates produced by Cufflinks and Sailfish show Pearson correlation coefficients that were all above 0.6, indicating a high level of confidence that Cufflinks FPKM values are comparable to other, reference-free quantification methods.
Within-sample pseudoreplicates of each biological replicate produced similar IDR profiles (Additional file 2: Figure S10), indicating similar data quality for each biological replicate.
This suggestion is based on a plausible assumption that the variation coefficient z ν is the same for the biological and technical replicates produced by a given biological experiment.
For each common bean tissue sample, three biological replicates were collected producing a total of 9 data points per probe (3 tissue types × 3 replicates).
For each tissue sample, three biological replicates were collected producing a total of 12 data points per probe (2 tissues × 2 genotypes × 3 replicates).
In a set of biological replicates, MAS5 produced inconsistent calls for twice as many probe sets as the GM algorithm.
In brief, 8 biological replicates were produced for each sample-type, and each sample was analysed using Taqman array cards, 384 well microfluidic arrays produced by Applied Biosystems.
Each cell line was cultured and passaged in the laboratory, and LMW RNA was isolated from a number of different passages so that four biological replicates were produced from each line.
Thus nanoCAGE-XL shows remarkably high reproducibility at single base resolution across biological replicates, and produces TSS peaks and peak modes comparable to those of PEAT despite a very different technical approach.
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