When I download the expresssion data GSE29609 from GEO database.
- 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).
- INV_VALUE is the opposite of VALUE.
- 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?
1 answer
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
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