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Differential Expression Analysis between Microarray and RNA-seq over Analytical Methods across Statistical Models

Wu, Yuhao
http://rave.ohiolink.edu/etdc/view?acc_num=case1586452969867803

Abstract Details

2020, Master of Sciences, Case Western Reserve University, EECS - Computer and Information Sciences.
Microarray and RNA-seq are two transcriptomics data types. Comparison between microarray and RNA-seq was popular in recent research fields. But few works analyzed both data types on the same sample groups and fewer have discussed whether different analytical methods or statistical models will impact on the results. To get an insight of what role analytical method and statistical model play, and also to eliminate variances that might be caused by data types, we applied microarray and RNA-seq data into 5 analytical methods across 4 statistical models to contrast the similarities and differences. In this thesis, we processed and transformed raw microarray and RNA-seq data to fit in 5 different analytical methods across 4 statistical models. We did differential expression analysis on both data for all methods and evaluated the results. Both data types showed high consistency in those two methods applying the same model. All statistical models gave similar detected differentially expressed genes, the extent of similarity varied basing on specific pairs chosen to be compared. Among all analytical methods, NBPSeq and NOIseq are the most consistent for microarray while DESeq and baySeq are the most consistent for RNA-seq. Between data types, RNA-seq gives more detected differentially expressed genes. Overall, statistical models and data types both impact greatly on differential analysis results while analytical method seems trivial.
Fredrick Schumacher (Committee Chair)
Jing Li (Committee Member)
Mehmet Koyuturk (Committee Member)
Satya Sahoo (Committee Member)
66 p.
Bioinformatics
microarray; RNA-seq; differential expression

Recommended Citations

Citations

  • Wu, Y. (2020). Differential Expression Analysis between Microarray and RNA-seq over Analytical Methods across Statistical Models [Master's thesis, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1586452969867803

    APA Style (7th edition)

  • Wu, Yuhao. Differential Expression Analysis between Microarray and RNA-seq over Analytical Methods across Statistical Models. 2020. Case Western Reserve University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1586452969867803.

    MLA Style (8th edition)

  • Wu, Yuhao. "Differential Expression Analysis between Microarray and RNA-seq over Analytical Methods across Statistical Models." Master's thesis, Case Western Reserve University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1586452969867803

    Chicago Manual of Style (17th edition)

case1586452969867803
609
© 2020, all rights reserved.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.