Severity: Warning
Message: fopen(/var/lib/php/sessions/ci_sessionft8lh9vsdocqdhl3brv4romqo3nmmk34): Failed to open stream: No space left on device
Filename: drivers/Session_files_driver.php
Line Number: 177
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Function: require_once
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Filename: Session/Session.php
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File: /var/www/html/index.php
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Function: require_once
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Message: Undefined array key "choices"
Filename: controllers/Detail.php
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File: /var/www/html/application/controllers/Detail.php
Line: 249
Function: _error_handler
File: /var/www/html/index.php
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Message: Trying to access array offset on value of type null
Filename: controllers/Detail.php
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File: /var/www/html/application/controllers/Detail.php
Line: 249
Function: _error_handler
File: /var/www/html/index.php
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Function: require_once
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Message: Trying to access array offset on value of type null
Filename: controllers/Detail.php
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Backtrace:
File: /var/www/html/application/controllers/Detail.php
Line: 249
Function: _error_handler
File: /var/www/html/index.php
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Function: require_once
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Message: Trying to access array offset on value of type null
Filename: controllers/Detail.php
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File: /var/www/html/application/controllers/Detail.php
Line: 249
Function: _error_handler
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Function: require_once
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Message: strpos(): Passing null to parameter #1 ($haystack) of type string is deprecated
Filename: models/Detail_model.php
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Function: strpos
File: /var/www/html/application/controllers/Detail.php
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Function: insertAPISummary
File: /var/www/html/index.php
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Function: require_once
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Filename: helpers/my_audit_helper.php
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Function: str_replace
File: /var/www/html/application/controllers/Detail.php
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Function: require_once
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Filename: controllers/Detail.php
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File: /var/www/html/application/controllers/Detail.php
Line: 256
Function: _error_handler
File: /var/www/html/index.php
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Message: Trying to access array offset on value of type null
Filename: controllers/Detail.php
Line Number: 256
Backtrace:
File: /var/www/html/application/controllers/Detail.php
Line: 256
Function: _error_handler
File: /var/www/html/index.php
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Function: require_once
Severity: Warning
Message: Trying to access array offset on value of type null
Filename: controllers/Detail.php
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Backtrace:
File: /var/www/html/application/controllers/Detail.php
Line: 256
Function: _error_handler
File: /var/www/html/index.php
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Function: require_once
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Message: Undefined array key "usage"
Filename: controllers/Detail.php
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Backtrace:
File: /var/www/html/application/controllers/Detail.php
Line: 257
Function: _error_handler
File: /var/www/html/index.php
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Message: Trying to access array offset on value of type null
Filename: controllers/Detail.php
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File: /var/www/html/application/controllers/Detail.php
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Function: _error_handler
File: /var/www/html/index.php
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Filename: controllers/Detail.php
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File: /var/www/html/application/controllers/Detail.php
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Function: _error_handler
File: /var/www/html/index.php
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Filename: controllers/Detail.php
Line Number: 258
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File: /var/www/html/application/controllers/Detail.php
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Function: _error_handler
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Filename: controllers/Detail.php
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Filename: controllers/Detail.php
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Filename: controllers/Detail.php
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Function: _error_handler
File: /var/www/html/index.php
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Filename: controllers/Detail.php
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Function: _error_handler
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Message: file_get_contents(https://...@gmail.com&api_key=61f08fa0b96a73de8c900d749fcb997acc09): Failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests
Filename: helpers/my_audit_helper.php
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File: /var/www/html/application/helpers/my_audit_helper.php
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Function: file_get_contents
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Function: simplexml_load_file_from_url
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Function: require_once
Background: With the exponential growth of high-throughput technologies, multiple pathway analysis methods have been proposed to estimate pathway activities from gene expression profiles. These pathway activity inference methods can be divided into two main categories: non-Topology-Based (non-TB) and Pathway Topology-Based (PTB) methods. Although some review and survey articles discussed the topic from different aspects, there is a lack of systematic assessment and comparisons on the robustness of these approaches.
Results: Thus, this study presents comprehensive robustness evaluations of seven widely used pathway activity inference methods using six cancer datasets based on two assessments. The first assessment seeks to investigate the robustness of pathway activity in pathway activity inference methods, while the second assessment aims to assess the robustness of risk-active pathways and genes predicted by these methods. The mean reproducibility power and total number of identified informative pathways and genes were evaluated. Based on the first assessment, the mean reproducibility power of pathway activity inference methods generally decreased as the number of pathway selections increased. Entropy-based Directed Random Walk (e-DRW) distinctly outperformed other methods in exhibiting the greatest reproducibility power across all cancer datasets. On the other hand, the second assessment shows that no methods provide satisfactory results across datasets.
Conclusion: However, PTB methods generally appear to perform better in producing greater reproducibility power and identifying potential cancer markers compared to non-TB methods.
Download full-text PDF |
Source |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10785356 | PMC |
http://dx.doi.org/10.1186/s12859-024-05632-w | DOI Listing |
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