Question: Spotfire: Issue when creating heat maps
0
gravatar for madkitty
5.6 years ago by
madkitty620
Canada
madkitty620 wrote:

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?

Thanks :) 

spotfire

 

 

heatmap microarray spotfire • 2.8k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 5.6 years ago by madkitty620

This does not answer your question directly, but have you considered using HeatmapGenerator (to plot the raw data, for example)?: http://sourceforge.net/projects/heatmapgenerator/

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Bohdan Khomtchouk320

Thanks, but we're tight to spotfire for this experiment. 

ADD REPLYlink written 5.6 years ago by madkitty620
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