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Users of the website can access microarray data available on the website (or upload their own microarray data), then use a variety of analytical methods, some of which we describe here for candidate gene searches using their own or published data on quantitative traits in panels of animals for which our site stores genetic and genomic data.
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Microarray data was then used to construct a molecular landscape, based on the mRNAs that were differentially expressed in the brains of BALB/cJ mice.
The microarray data were then analyzed by SAM.
The LIMMA algorithm (linear models for microarray data) was then used to identify transcripts differentially expressed between the leukocyte population and the liver reference data.
The microarray data were then examined for expression of a large panel of markers identified in Sherwood et al. that are described as distinguishing between DE and VE (Fig. 5).
These approaches first identify differentially-expressed genes within microarray data, and then evaluate the performance of pre-defined functional gene categories (or networks) to identify the genes that associate with the phenotype of interest (see [9] for a comprehensive review of these approaches).
Microarray data were then analyzed using the Bioconductor Limma package.
Microarray data were then analyzed by two different approaches.
The microarray data were then normalized by quantile normalization and logarithmically transformed before further analysis.
Microarray data was then interrogated with the MetaCore software suite from Thomson Reuters.
Microarray data were then validated through quantitative real-time PCR (qPCR) (see Methods).
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