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The development of predictors began with individual microarray comparisons using the liver tissue.
Microarray comparisons using RNA from the following genotypes were performed: wild type males and females from two different strains (CS and Berlin), male and female tud progeny, wild type females and tra pseudomales, and wild type females and dsx D pseudomales.
Microarray comparisons using RNA derived from sex determination hierarchy mutants were conducted with four replicates, with a dye-swap design; i.e. cDNA from each genotype contained incorporated Cy3-labeled dUTP in two experiments and contained incorporated Cy5-labeled dUTP in the other two experiments.
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The value of this approach is two-fold: first, we incorporate textual data into the process of microarray comparison, using a new source of data to better judge array similarity; additionally, we improve the performance of existing expression level similarity models by providing additional, algorithmically selected labeled data.
This comparison highlights the difficulty of inter-species comparisons using microarray technology, a limitation that is compounded by the lack of complete genomes for both S. japonicum and S. mansoni and the absence of comprehensive bioinformatics comparisons at the genomic level.
Genomic comparisons using microarrays permit the detection of candidate pathogenicity genes on the basis of their consistent presence in invasive and their absence from less virulent organisms.
Large-scale comparisons using microarrays found that some experimental parameters were more critical than others in the analysis and interpretation of gene expression data.
In inter-strain comparisons using microarrays, mRNA differences between the strains might result in differences in hybridisation efficiency which from the array data alone cannot be distinguished from expression level differences.
The Student's t-test was used for statistical comparisons, and P-values obtained from the microarray were adjusted for multiple comparisons using the false discovery rate correction, in order to obtain an adjusted Q-value for each observation.
In terms of global gene and protein expression profiling, comparisons using cDNA microarrays and two-dimensional electrophoresis revealed high consistencies between multiclonal ASC and BMSC cultures (Refs 52, 62, 63).
Overall, smaller magnitude differences were seen within the comparisons using the miRNA microarrays as compared to the genomic expression microarrays.
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