Hivanson Week 9

Begin by recording in your wiki, the strain that you will analyze, the filename, the number of replicates for each strain and each time point in your data.

Strain name: ∆CIN5 strain

Filename: HI_BIOL367_S24_microarray-data_dCIN5.xcls

Number of replicates per strain: 4

Timepoints: 15 minutes, 30 minutes, 60 minutes, 90 minutes, 120 minutes

How many genes have p < 0.05? and what is the percentage (out of 6189)?

2290 genes; 37.0%

How many genes have p < 0.01? and what is the percentage (out of 6189)?

1380 genes; 22.3%

How many genes have p < 0.001? and what is the percentage (out of 6189)?

691 genes; 11.2%

How many genes have p < 0.0001? and what is the percentage (out of 6189)?

358 genes; 5.8%

How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?

151 genes; 2.4%

How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?

1453 genes; 23.5%

Find NSR1 in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment?

Unadjusted p value: 6.37625E-08

Bonferroni-corrected p value: 0.000394626

B-H-corrected p value: 2.19237E-05

average Log fold change @ 15 minutes: 4.070025

average Log fold change @ 30 minutes: 3.611475

average Log fold change @ 60 minutes: 4.2985

average Log fold change @ 90 minutes: -2.900925

average Log fold change @ 120 minutes: -0.9315

NSR1 shows increased expression from time 15 minutes through 60 minutes. At 90 minutes, NSR1 expression decreases, and at 120 minutes, the expression of NSR1 remains decreased.

Unadjusted p value: 0.111670609

Bonferroni-corrected p value: 1

B-H-corrected p value: 0.232000469

average Log fold change @ 15 minutes: 1.638433333

average Log fold change @ 30 minutes: -0.100766667

average Log fold change @ 60 minutes: 1.659233333

average Log fold change @ 90 minutes: -0.608333333

average Log fold change @ 120 minutes: -0.168133333

Excel microarray data

p value table slide for ∆CIN5

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