I used 45K rice slide in my experiment and need to analyze the data using limma package in bio-conductor. Can anyone lend advice on this topic? Does anyone have experience with the GUI bio-conductor? Is there a better way to analyze this data?
Check the manual of the limma package, since the commands that will be needed to run the analysis tool are already given in the correct order. Just you will download R and Bioconductor to your computer and then you should follow the instructions given in the manuals. If you give more information about your objectives, I may recommend you more user-friendly software for statistical analysis.