I'm having a hard time retrieving the most expressed genes in a cell line. One of the databases I've found has values for a lot of genes in 60 different cell lines and it seems the data is obtained using GC-RMA. The data is available here in the file NCI60_U133A_20070815.raw.csv.

My problem is what does the values actually represent? Would it be correct to assume the genes with high values are the ones most expressed in the corresponding cell line?

I've found a short explanation on why there is no unit definition on the page here.

Here is a snapshot of the file:

-            huh-7    huh-7      HEK293  ...
1007_s_at    31.727    55.551    360.731
1053_at     402.633   441.622    557.782
117_at        9.968    10.178      9.565

These values come from a microarray so they represent the number of sequences that where attached to the microarray's probes (1007_s_at, ...).

In general yes, a higher value means more expression. The normalizations (GC-RMA) applied are to correct for several effects. They help for testing the probability of the given probe to be a false positive.


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