A Microarray Data Pre-processing Method for Cancer Classification
The development of microarray technology has led to significant improvements and research in various fields. With the help of machine learning techniques and statistical methods, it is now possible to organize, analyze, and interpret large amounts of biological data to uncover significant patterns o...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Politeknik Negeri Padang
2022-12-01
|
| Series: | JOIV: International Journal on Informatics Visualization |
| Subjects: | |
| Online Access: | https://joiv.org/index.php/joiv/article/view/1523 |
| _version_ | 1827998717805854720 |
|---|---|
| author | Tay Xin Hui Shahreen Kasim Mohd Farhan Md Fudzee Zubaile Abdullah Rohayanti Hassan Aldo Erianda |
| author_facet | Tay Xin Hui Shahreen Kasim Mohd Farhan Md Fudzee Zubaile Abdullah Rohayanti Hassan Aldo Erianda |
| author_sort | Tay Xin Hui |
| collection | DOAJ |
| description | The development of microarray technology has led to significant improvements and research in various fields. With the help of machine learning techniques and statistical methods, it is now possible to organize, analyze, and interpret large amounts of biological data to uncover significant patterns of interest. The exploitation of microarray data is of great challenge for many researchers. Raw gene expression data are usually vulnerable to missing values, noisy data, incomplete data, and inconsistent data. Hence, processing data before being applied for cancer classification is important. In order to extract the biological significance of microarray gene expression data, data pre-processing is a necessary step to obtain valuable information for further analysis and address important hypotheses. This study presents a detailed description of pre-processing data method for cancer classification. The proposed method consists of three phases: data cleaning, transformation, and filtering. The combination of GenePattern software tool and Rstudio was utilized to implement the proposed data pre-processing method. The proposed method was applied to six gene expression datasets: lung cancer dataset, stomach cancer dataset, liver cancer dataset, kidney cancer dataset, thyroid cancer dataset, and breast cancer dataset to demonstrate the feasibility of the proposed method for cancer classification. A comparison has been made to illustrate the differences between the dataset before and after data pre-processing. |
| first_indexed | 2024-04-10T05:47:07Z |
| format | Article |
| id | doaj.art-0c929d71c46a4fca98c50085d028bc1d |
| institution | Directory Open Access Journal |
| issn | 2549-9610 2549-9904 |
| language | English |
| last_indexed | 2024-04-10T05:47:07Z |
| publishDate | 2022-12-01 |
| publisher | Politeknik Negeri Padang |
| record_format | Article |
| series | JOIV: International Journal on Informatics Visualization |
| spelling | doaj.art-0c929d71c46a4fca98c50085d028bc1d2023-03-05T10:28:41ZengPoliteknik Negeri PadangJOIV: International Journal on Informatics Visualization2549-96102549-99042022-12-016478479010.30630/joiv.6.4.1523444A Microarray Data Pre-processing Method for Cancer ClassificationTay Xin Hui0Shahreen Kasim1Mohd Farhan Md Fudzee2Zubaile Abdullah3Rohayanti Hassan4Aldo Erianda5Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, MalaysiaUniversiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, MalaysiaUniversiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, MalaysiaUniversiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, MalaysiaUniversiti Teknologi Malaysia, 83100, Johor, MalaysiaPoliteknik Negeri Padang, Sumatera Barat, IndonesiaThe development of microarray technology has led to significant improvements and research in various fields. With the help of machine learning techniques and statistical methods, it is now possible to organize, analyze, and interpret large amounts of biological data to uncover significant patterns of interest. The exploitation of microarray data is of great challenge for many researchers. Raw gene expression data are usually vulnerable to missing values, noisy data, incomplete data, and inconsistent data. Hence, processing data before being applied for cancer classification is important. In order to extract the biological significance of microarray gene expression data, data pre-processing is a necessary step to obtain valuable information for further analysis and address important hypotheses. This study presents a detailed description of pre-processing data method for cancer classification. The proposed method consists of three phases: data cleaning, transformation, and filtering. The combination of GenePattern software tool and Rstudio was utilized to implement the proposed data pre-processing method. The proposed method was applied to six gene expression datasets: lung cancer dataset, stomach cancer dataset, liver cancer dataset, kidney cancer dataset, thyroid cancer dataset, and breast cancer dataset to demonstrate the feasibility of the proposed method for cancer classification. A comparison has been made to illustrate the differences between the dataset before and after data pre-processing.https://joiv.org/index.php/joiv/article/view/1523data pre-processingmicroarray datagene expression datagenepattern. |
| spellingShingle | Tay Xin Hui Shahreen Kasim Mohd Farhan Md Fudzee Zubaile Abdullah Rohayanti Hassan Aldo Erianda A Microarray Data Pre-processing Method for Cancer Classification JOIV: International Journal on Informatics Visualization data pre-processing microarray data gene expression data genepattern. |
| title | A Microarray Data Pre-processing Method for Cancer Classification |
| title_full | A Microarray Data Pre-processing Method for Cancer Classification |
| title_fullStr | A Microarray Data Pre-processing Method for Cancer Classification |
| title_full_unstemmed | A Microarray Data Pre-processing Method for Cancer Classification |
| title_short | A Microarray Data Pre-processing Method for Cancer Classification |
| title_sort | microarray data pre processing method for cancer classification |
| topic | data pre-processing microarray data gene expression data genepattern. |
| url | https://joiv.org/index.php/joiv/article/view/1523 |
| work_keys_str_mv | AT tayxinhui amicroarraydatapreprocessingmethodforcancerclassification AT shahreenkasim amicroarraydatapreprocessingmethodforcancerclassification AT mohdfarhanmdfudzee amicroarraydatapreprocessingmethodforcancerclassification AT zubaileabdullah amicroarraydatapreprocessingmethodforcancerclassification AT rohayantihassan amicroarraydatapreprocessingmethodforcancerclassification AT aldoerianda amicroarraydatapreprocessingmethodforcancerclassification AT tayxinhui microarraydatapreprocessingmethodforcancerclassification AT shahreenkasim microarraydatapreprocessingmethodforcancerclassification AT mohdfarhanmdfudzee microarraydatapreprocessingmethodforcancerclassification AT zubaileabdullah microarraydatapreprocessingmethodforcancerclassification AT rohayantihassan microarraydatapreprocessingmethodforcancerclassification AT aldoerianda microarraydatapreprocessingmethodforcancerclassification |