What is the expression value of GSE29609 in GEO database

Question

[keke]

When I download the expresssion data GSE29609 from GEO database.

1. There are two values could be found for each sample, namely, VALUE(-INV_VALUE: normalized Cy3/Cy5) and INV_VALUE(normalized log10 ratio Cy5/Cy3).
2. INV_VALUE is the opposite of VALUE.
3. When download the data using GEOquey, the VALUE was returned.

My question is, comparing INV_VALUE (normalized log10 ratio Cy5/Cy3) is much more likely to the true expression. Why the VALUE is returned?

Could I trust the VALUE as the true expression?

Answer 1

[Kevin Blighe]

Hi keke, Cy5 / Cy3 would be the more standard way to do it - GEOquery will just work with whatever data the authors have uploaded. If this is Cy3 / Cy5, then so be it. It looks okay and ready to use:

If you wanted, you could download the raw files and process these yourself. I posted some code here for two-color Agilent arrays: build the expression matrix step by step from GEO raw data

Please also check the limma manual, where there is a dedicated section for this (I believe).

Kevin