Dec 29th

• The whole morning is spent on modifying the Piano code, whose draft has already been done yesterday! The main problem lies in the file directory, which is stupid and costs much more time than it should...

  Code: 10_Piano3.R
  Results: Piano_GO_HS.xls, Piano_HS_KEGG.xls, Piano_NC_GO.xls, Piano_NC_KEGG.xls, Piano_SN_GO.xls, Piano_SN_KEGG.xls.

• Read into Piano's function of building pathway networks and heatmaps, thinking about doing that.
• As the literature searching task is as important, I took Dimitri's Piano result for this, because mine results haven't been ready yet.

  In this part I am assigned to validate the enriched pathways from NASH to HCC. I extracted N->C enriched pathways in KEGG and GO, respectively, in Dimitri's results. I also divide the up- and down-regulated pathways into two sets for the ease of investigation. I marked out the genes that have FDR<5% and ranked them (but they are so many, even after filtering out regulated under a certain direction...)