http://postimg.org/image/5by31nkyp/When creating a heatmap on spotfire, I follow the steps recommended by a biostar users:
File > Add Data Table > From (txt file) > Select Unpivot transformation > Select Gene column as Passthrough and select Cell columns as Columns to Transform.
Click OK to add the unpivoted tall-narrow table. My table has 3 columns: Gene, Category (Cell), and Value, then I add the heat map:
Insert > New Visualization > Heat Map, and visualize the new unpivoted data table > Set the row selector to Gene; the column selector to Category (Cell).
However, at the bottom of the heatmap it says Average(count), I don't understand what this function does.. also I only want to represent 3 heatmaps with 1) the raw data 2) log2 normalized 3) log2 + P90 normalized.
Can anyone explain to me what does the Average(count) does and how can I display only the raw data (without any average or anything like that). Also, how do I log2 normalized and the 90th percentile normalization on the data?