I'm a beginner in microarray analysis. I have an excel file with RMA normalized expression values: with probe IDs as rows and my RNA samples as columns. I can use this for GSEA, etc.. , but it seems that for analysis with limma in R, I would need the raw files and normalize them with affy in R. Is it possible to use my already normalized data as input for limma in R? How does my (txt) file need to look like? And can I import also a targets file, with only relevant clinical information, and not the Cy3 and Cy5 columns?
I apologize for this beginners question and hope you can help me.