What do the red bars and blue squares represent in GEO profile charts?
In GEO Profile charts, the red bars represent values extracted from original GEO Sample records as supplied by submitters. For single channel data, values are assumed to be submitted as normalized signal count data, reflecting the relative measure of abundance of each transcript. For Affymetrix data, the “detection call” (A=absent, P=present, M=marginal) data are taken into consideration, if supplied (absent calls faded out). For dual channel experiments values are normalized log ratios, and SAGE values reflect “tags per million” counts. The blue squares represent the percentile ranked value of a spot compared to all other spots within that Sample. That is, all values within each Sample are rank ordered and placed into rank percentile ‘bins’. This gives an indication of the relative expression level of that gene compared to all other genes on the array. Value profiles are plotted on a scale that fits each individual gene, whereas rank data are always plotted on a scale of 0-100%.
