However, datasets used as prior information and validation gold standards are often related and limited to a subset of genes. This lack of complete and independent evaluation calls for new criteria to robustly estimate the optimal intensity of prior data integration in...
Although PA methods have been developed and used for well over a decade, there still exist a limited number of formal assessments and comparisons of tools and algorithms. There are several reviews [17,23] and benchmark [10,22,24,25] articles published offering guidance on the selection of PA...
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In addition, to ensure that the methods in the methylGSA package produced reasonable output, we limited the size of the gene sets to those with at least 5 and at most 5000 genes in the set. If these additional constraints are not included, the methylGSA methods mGLM and mRRA (ORA) ...
thereby mitigating its influence on the factors. The ability to incorporate cell-type-specific factors guides inference. For example, the T cell antigen receptor (TCR) activation program should be limited to T cells, but many of its genes are activated by additional programs in other cell types...
Most newly identified genes are detected in a limited number of experimental conditions (Figure 5), even if the RT-PCR results may show a basal level of transcripts due to a higher sensitivity. Indeed, 40% of the novel genes have been detected in 1 to 5 mRNA samples while there are ...
Effective utilization of these datasets has, however, been limited because of a shortage of suitable tools to integrate large-scale and diverse microarray datasets. In most common use case, a scientist performs an experiment-based analysis: he or she downloads microarray data and sample annotations...
Results We developed a statistical way, based on the concept of confidence interval, to determine the minimum support and minimum confidence for mining association relationships among items. With the minimum support and minimum confidence, one can find significant rules in one single step. The DAR ...
Also, limited numbers of tissue-specific EST and mRNA sequences deposited into public databases, as well as different cDNA construction protocols may miss tissue-specific transcript constructs [10]. Again, biological experiments may be necessary to confirm any transcript constructions, but programs which...
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