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Examples of the similarity in expression signal between replicate samples is shown in Supplementary Material, Figure S4, for highly correlated replicates (left column), moderately correlated replicates (middle column) and poorly correlated replicates (right column).
Figure 2 b shows the correlation of microRNA expression between D. virilis and D. melanogaster stages averaged between replicates (left), and the ranges of these values between individual data sets (right; heatmaps for all-versus-all data sets are presented in supplementary fig. S2, Supplementary Material online).
Fig. 2 shows that, for two-person mixtures, the analysis assuming one-contributor-plus-dropin gave a very good approximation for the lab-based replicates (left panels), and a reasonably good approximation for the simulation replicates, but with more variable ltLR values, as indicated by the wider range.
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Further, the overall balance of small and large footprints varied between replicates, leaving open the question of which conformation is more populated in vivo.
RNA from five biological replicates leaves, hypocotyls, and roots from spaceflight (FLT) and ground control (GC) samples were analyzed using ten Affymetrix GeneChip® Arabidopsis ATH1 Genome Arrays (A-AFFY-2).
Leaf material was sampled in accordance with Cornelissen et al. (2003) with 10 replicate leaves collected from each zone.
For analysis of asexual fungal sporulation, 8 12 replicate leaves from independently inoculated wheat seedlings randomly distributed in a walk-in temperature, humidity and light-controlled artificial environment were collected at either 21 or 34 days post inoculation (DPI).
Clones with less than 25% of replicate features left and the 3% of clones with the highest across-replicate-feature SD of log2 [cy3/cy5] were removed from further analysis.
The program edgeR was used with the "calcNormFactors" function to identify DEGs between drought and WW conditions in: 1) leaves of genotype 592 (five replicates), 2) leaves of genotype 520 (five replicates), 3) root tips of genotype 592 (four replicates) and 4) root tips of genotype 520 (four replicates).
Each treatment was repeated three times, two of five rows from each replicate were left for squash seed production.
One of these failed samples was a technical replicate, which left 198 tumour samples for analysis.
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