Am trying to do DEG analysis in limma. Since am new to this i want to know how to normalize the data(GEO GSE matrix file). My data contains different time course samples (control and diseased) . I want to do DEGs at different time point within the data.Can anyone suggest me codes to run GEO matrix file in Rstudio using limma.
Nobody can 'suggest codes' to run an analysis on some unspecified GEO data. Analyzing data isn't a commoditized process where you can get some basic code off the internet and then get it done.
There is a vignette for the GEOquery package that shows examples of how you would get the data, and there are any number of examples in the limma User's Guide that show how to use limma to analyze different data sets. If you have specific questions about some of the steps required to do the analysis, you could show what you have done and ask about that, or you could ask about particular steps that you might not understand.
This support site is intended to help people who are having technical problems with Bioconductor packages. Your question has to do with how you should analyze your data. As the analyst, it's up to you to decide such things. If you don't know, there are any number of sources you could read that explain how to analyze microarray data, and you should find and read those. Alternatively you could find somebody local to help you. Answering questions about how to analyze data is beyond the scope of this site, so you will in general not find help for that here.
Thank you for your reply James. do i want to do normalization for GSE matrix file.
This support site is intended to help people who are having technical problems with Bioconductor packages. Your question has to do with how you should analyze your data. As the analyst, it's up to you to decide such things. If you don't know, there are any number of sources you could read that explain how to analyze microarray data, and you should find and read those. Alternatively you could find somebody local to help you. Answering questions about how to analyze data is beyond the scope of this site, so you will in general not find help for that here.