Joe, Pathview take data in any scale, either relative or absolute levels. But you need to make sure the limit argument is properly set. Pathview doesn?t do time-course or multi-state/sample in the same graph at this time. you can generate one graph for each sample. It will plot time- course or multi-state/sample in one graph soon in next version. HTH, Weijun -------------------------------------------- On Wed, 9/11/13, joseph.houjue wrote: Hey Weijun, ? I have a question about data format. The input data should be normalized intensity or log normalized intensity? or FoldChange?? and the value is mean of each group? or individual sample? If I have time-course data, how could I present multi-time points in one map? ? Thanks, Joe ?