Kevinmcgee Week 13

• Opened L.infantumCompliedRawData(A).txt
• Finished the formatting by flipping the dye swap chips negative
• Created a column next to dye swap chips and did the formula:

=-1*(dye swap chip column)

• made a new sheet
• added all data from old sheet except only added the flipped dye swaps
• looked for background information in the array paper
  • L. infantum MHOM/MA/67/ITMAP-263 and L. major LV39 MRHO/SU/59/P strains used in this study
  • All microarray data will be freely available on the Geo NCBI database in the MIAME format
    • The series accession number for our manuscript is GSE10407.
  • Each chip compares promastigote vs. amastigote with different replicates
  • Following data files found

• Finished naming sheet with helpful names to know what is what on the sheet
• Ready for statistical analysis
• Began analysis by taking the average and standard deviation of our data chips seperately and using that information to scale and center our data:

=(B4-B$2)/B$3 This shows the equation we used to scale and center.

• Copied and pasted values of scaled centered onto a new page. From there, we edited out all VALUE! cells and left them blank. GenMAPP will ignore these blanks when we input our data.
• Made a column of the average fold change for each gene call Avg_LogFC_All

Average B2:G2

• Made a column of the Tstat and Pvalue for the fold changes of each gene:

=AVERAGE(B2:G2)/STDEV(B2:G2)/SQRT(6) TStat
=TDIST(ABS(I2),5,2) Pvalue

• Created a new page titled forGENMAPP
  • Copied and pasted all values from statistics page
• Cut and pasted columns H-J and moved them to columns B-D
• Inserted a new column at B called System Code. Filled in column with the letter N
• File is now ready for GenMAPP import

• Sample of what the final file looked like