I am new in analyzing expression data (I have a computer science background). My objective is to reconstruct a gene regulatory network. To do so I want to combine different series (If it is possible) from GEO in order to have a larger dataset (with enough samples). So I have to work with raw dat and normalize it by myself. I went on GEO and I find out that there are different type of file : .CELL, .GPR, .CSV, .TXT and so on. Those files have different headers (in the matrix data) : such as "Chx Log Ratio" or ''Chx mean" "Chx Median" etc ; For the .GPR files the headers are for example "F633 Median" or "F543 Median" etc. My questions are :
1-Can I combine several series from GEO (I don't want to perform differentially expressed genes)?
2- Does anyone know any links that explain the different heading depending on the file's type?
3- As I want to normalize the data by myself which columns ( headers) should I consider depending on the file's type?
Thanks you very much.