Volume: 2, 2023
2nd International PhD Student’s Conference at the University of Life Sciences in Lublin, Poland:
ENVIRONMENT – PLANT – ANIMAL – PRODUCT
Abstract number: T039
DOI: https://doi.org/10.24326/ICDSUPL2.T039
Published online: 19 April 2023
ICDSUPL, 2, T039 (2023)
Selected statistical methods in plant experiments based on RNA-seq technology
Grażyna Niedziela1*, Alicja Szabelska-Beręsewicz1, Joanna Zyprych-Walczak1, Małgorzata Graczyk1
1 Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznań, Poland
* Corresponding author: grazyna.niedziela@up.poznan.pl
Abstract
RNA-seq technology based on transcriptome sequencing is used in particular in differential expression studies. Many analyzes using RNA-seq technologies relate to medical or animal data. There are far fewer agricultural datasets in publicly available sequencing repositories. That is why statistical approaches used in RNA-seq data will be adopted for a number of plant data. There exist many statistical methods used for seeking genes that differentiate between two or more conditions, causing scientists to often ask which method to use. In an attempt to answer this question in the field of plant RNA-seq data, the two most popular methods of differential analysis will be presented: edgeR and DESeq2. We evaluated these methods based on four real RNA-seq plant experiments. The conclusions drawn from the comparative analysis will support the scientists’ decisions regarding the choice of method. The results indicate that there is a large intersection between the lists of differentially expressed genes produced by the two methods. However, depending on the research goal and the preparation of an experiment, different approaches to statistical analysis and interpretation of the results can be suggested. One of the approaches would be to use both the edgeR and DESeq2 methods during the statistical analysis, and to give as the final result the intersection of the two lists of differentiating genes. Attention should also be paid to the need of investigation of the diagnostic plots, which can show the advantages and disadvantages of using a given method in a specific dataset.
How to cite
G. Niedziela, A. Szabelska-Beręsewicz, J.Zyprych-Walczak, M. Graczyk, 2023. Selected statistical methods in plant experiments based on RNA-seq technology. In: 2nd International PhD Student’s Conference at the University of Life Sciences in Lublin, Poland: Environment – Plant – Animal – Product. https://doi.org/10.24326/ICDSUPL2.T039