Kara M Dismuke Week 11 Journal

Electronic Journal Notebook

• Project Partner: Kristen Horstmann
• Dahlquist lab microarray data set: Wild type vs. Δzap1
  • Note: Kristen will be analyzing the Wild type strain data and I (Kara) will be analyzing the Δzap1 strain data.

• For Δzap1...[File: Dahlquist_Lab_Microarray_Data_dZAP1_20150319_KMD]
  • • t15: 4 replicates
    • t30: 4 replicates
    • t60: 4 replicates
    • t90: 4 replicates
    • t120: 4 replicates
• Procedural Notes:
  • After downloading the data, we used Excel to compute the averages of our data from the replicates from each time point for each gene.
    • column headings: "zap1_xbar_t15", "zap1_xbar_t30", "zap1_xbar_t60", "zap1_xbar_t90", "zap1_xbar_t120"
  • Then we computed the "grand" average for all of our data for a particular gene. For the case of Δzap1, this could be computed by averaging all the data (this is contains all the data at each time point) or by averaging the averages previously connected because there were 4 replicates for each time point. If done both ways, you should get the same value.
  • column heading: "zap1_xbar_grand"
  • We used Excel to compute the sum of squares for the data for each individual gene.
    • column heading: "zap1_ss_HO"
  • For each time point, we calculated the sum of squares by squaring the original data, and then subtracted from this the replicates times the average of the time point's data squared.
    • column headings: "zap1_ss_t15", "zap1_ss_t30", "zap1_ss_t60", "zap1_ss_t90", "zap1_ss_t120"
  • Then, we took these calculated values for each time point and found the average of them.
    • column heading: "zap1_SS_full"

unadjusted p value <.05

• wild-type: 31.42% (2378/6189)
• dzap1: 36.58% (2264/6189)

unadjusted p-value < .01

• wild-type: 24.67% (1527/6189)
• dzap1: 23.35% (1445/6189)

unadjusted p-value < .001

• wild-type: 13.90% (860/6189)
• dzap1: 12.80% (792/6189)

unadjusted p-value < .0001

• wild-type: 7.43% (460/6189)
• dzap1: 6.69% (414/6189)

Benjamini & Hochberg-adjusted p-value < .05

• wild-type: 26.76% (1656/6189)
• dzap1: 24.85% (1538/6189)

Bonferroni-adjusted p-value <.05

• wild-type: 3.68% (228/6189)
• dzap1: 3.10% (192/6189)

• Note: We've organized this data into a table in a PPT slide: Table 1 (wildtype and dzap1 p-values)‎