GEO profiles - (Oct/28/2005 )

Hallo,

I have a question about the data that can be found in the NCBI database GEO profiles (gene expression data). When quering for a gene, I can receive a list of results that are represented in graphs showing the expression level of a gene (in different tissues) using arbitrary units. Can anyone please explain how are the arbitrary units (red bars) calculated and explain in a more simple way than in the GEO website what do the blue squares mean?

thank you!

Hi,

The help file is here

http://www.ncbi.nlm.nih.gov/projects/geo/gds/graph_cap.html

Thanks, I`ve red that through already before:) Please tell me if i understand that right.
For example the help file says:
"Red bar: Represents value measurements as extracted from original submitter-..... and reflect the measured level of abundance of an individual transcript..... Values are presented as arbitrary units.

"for the single channel experiment - values are assumed to be submitted as normalized (scaled) signal count data. These data are then log2-transformed by our systems for better data distribution"

So to my understanding the red bar - arbitrary unit - is X in the equation of X=log2(Y), where Y is the normalised value from the submitter. Am I right?

and about the blue squares:)
can you please explain what is rank ordering in this respect?(I`m not a native English speaker so have some problems:)

thank you!