Question: Raw files from GEO
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gravatar for kamgnia.phanie
3.5 years ago by
Canada
kamgnia.phanie0 wrote:

Hello,

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.

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