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Scatter plots were also generated using this software to inspect the reproducibility of the replicates as well as the degree of variations of the samples under comparison.
GAGE [ 18] was applied to infer the most differentially expressed pathways or gene sets between the BMP6 added or withdrawn samples under comparison at different time points.
The individual replicates of the samples under comparison are taken together, normalized and the mean relative OD per time point is calculated.
When studying mixed cell populations, gene expression profiling can successfully detect differential gene expression in specific cell types present in the samples under comparison.
The relative intensity of each reporter ion in that cluster is then used to give a measure of the relative abundance of that peptide between the six samples under comparison.
The ratio controls (which are detected using 'spikes' of different ratios of probe between the two hybridization samples under comparison, see below) measure different ratios of gene expression, over a range of 2.5 orders of magnitude.
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Equal amounts of protein are used for each sample under comparison so that any differences in relative peptide/protein amount measured by mass spectrometry reflect differences between samples, not starting protein amounts.
For any given contrast, either between breeds or time points, genes flagged as lowly expressed in more than half of the microarrays in all sample groups under comparison were filtered out.
Whenever sampling was incomplete in one data set under comparison, the data set that sampled more months was truncated to match the sampling period of the shorter data set.
For SFP detection, we applied the RPP method to each probe set that had a "present" call in all chip samples from each pair of genotypes under comparison: (1) Pokkali versus IR29, (2) Pokkali versus FL478, (3) IR29 versus FL478.
Table 3 shows increase in compressive strength for internally cured samples in comparison with control samples under similar curing conditions.
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