ArrayMining

[…] on r environment (http://www.r-project.org/). to remove the non-biological experiment variation across different microarray individuals, ailun [] platform comparison (http://ailun.stanford.edu/) and arraymining [] cross-study integration (http://www.arraymining.net/) were achieved as our previously described []., as a major challenge for gene signatures identification, limited sample of clusters […]

[…] all analyses reported used the ‘quantile’ normalisation method with background correction within genomestudio., bioinformatics analysis of differentially expressed genes was performed using the arraymining software [] with the empirical bayes moderated t-test method. significant difference in expression was determined by fdr corrected p-value from multiple t-tests < 0.05. microarray data […]

[…] was the corresponding value that optimize f1-score at default., ensemble class assignment analyses on the corresponding data sets of the whole transcriptome information were conducted using arraymining online software []. in brief, the data set was introduced to the class assignment module with the settings of the ensemble method for feature selection. the ensemble method […]

[…] cholera toxin and 10% matrigel for up to 7 days, with medium changed every other day., for the analysis of the homeobox gene array, hierarchical cluster analysis was performed by using the software arraymining (http://www.arraymining.net/). venn diagrams were generated with the online tool venny (http://bioinfogp.cnb.csic.es/tools/venny/index.html)., the analysis of copy number variation […]

[…] genes by taking the mean of all probes that corresponds to the same gene. the missing values were eventually replaced using the knn algorithm., bioinformatics analysis was completed by applying arraymining software (http://www.arraymining.net/) and the cytoscape package. the transcriptome analysis for microarrays was carried out using complementary approaches: a david analysis […]

[…] relative values between the cell lines. the sample gene profile file was then annotated using hg18 prior to performing differential gene expression analysis (dgea)., the dgea was performed using arraymining, an online microarray data mining software package []. differential gene expression was conducted using sam analysis to list genes differentially expressed with respect to treatment […]