Difference between revisions of "Kevinmcgee Week 13"

Revision as of 18:53, 21 November 2013

• 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

7Ready for statistical analysis 7Began 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