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Meta-analysis of gene expression microarray datasets presents significant challenges for statistical analysis.
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For example, by including a large number of additional Populus leaf microarray datasets present in UPSC-BASE (e.g. after drought stress, herbivore and pathogen treatments, cold treatments, diurnal cycles etc).
While the microarray dataset presented in this manuscript was newly generated and first reported in this study, it is also a most recent report from a series of pathogen-host interaction studies completed by our research group.
Among them, Gene Expression Omnibus (GEO) provides most profuse microarray expression datasets presented with the function of GEO DataSets, GEO Profiles, and GEO2R Analysis [ 13].
One miRNA microarray dataset was presented by Baskerville et al. [14], the other was obtained from Barad et al. [27].
A complete microarray dataset is presented in Aditional file 2: Table S3.
The microarray datasets are usually presented in 2D matrices, where rows represent genes and columns represent experimental conditions.
A larger database was constructed from 1305 available raw microarray datasets (Additional file 19) present in NASC affyarrays and the gene expression omnibus.
At present, five microarray datasets (Table 2) containing data from normal and gastric cancer tissues were available in GEO website.
As the noise is present in microarray datasets, the deviation from actual value and expected value of each element in the dataset also exists.
As one of a variety of measures proposed to capture the data complexity of GEPs, F-ratio statistic varies in its degree of correlation with the performance of classifiers[ 11, 12, 14], probably because of a wide range of linear separability present among microarray datasets [ 13].
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