Question: running GEO series matrix file normalization and DEGs in limma
gravatar for devarajsaranya
5 days ago by
devarajsaranya0 wrote:

hello everyone

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. 

Thank u.

ADD COMMENTlink modified 4 days ago by James W. MacDonald46k • written 5 days ago by devarajsaranya0
gravatar for James W. MacDonald
4 days ago by
United States
James W. MacDonald46k wrote:

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.

ADD COMMENTlink written 4 days ago by James W. MacDonald46k

Thank you for your reply James. do i want to do normalization for GSE matrix file. 

ADD REPLYlink written 1 day ago by devarajsaranya0

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.

ADD REPLYlink written 23 hours ago by James W. MacDonald46k
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