R Packages to Identify Differentially Expressed Genes - Coursework Example

Data calling and testing:
This is the stage at which the data file in Excel (comma delimited) is made available in R. the calling function is used and the data is classified in an orderly time series sequence for further

Application of Significance analysis packages:
The three R significance analysis packages; t-tests, eBayes and SAMr are used to test whether there are significantly differentially expressed genes among those listed. Where such are noticed they are recorded.

Check for consistency:
This stage involved the determination of whether the results for each individual test were consistent all through. This is proof of the accuracy of each method as compared to the others.

Generation of supportive diagrams:
Venn diagrams and volcano plots of the p-values were generated in the final phase. The purpose of the Venn diagram is to illustrate the mathematical positions of the individual tests are also highly interactive.
Owing to time constraints, some important operations that would have allowed the analysis to exhibit more of its features were left out. For example, the arrays were given a summative test at every level; that is t-tests, Bayes, and same. The arrays would have exhibited more underlying relations if the individual cases were matched against their resultant gene expressions after the administration of the drug.
Using this approach, paired samples t-tests would have been the convenient tests, which would also require such specifications on the instructions page.
The columns could alternatively have been split up in pairs to come up with several individual files that would allow the execution of singular tests on individual files, thereby making the results even more focused. The only weakness of this approach is the need to further recombine the individual results from the tests, which can not be addressed by the use of the combined arrays.

This sets a crucial precedent especially since the same method of study will be repeated for future tests.
With further incorporation of more packages of R, it is possible to carry out more relevant studies and compare the results obtained for proof of consistency. Read More