# James P. McDonald Week 9

(Difference between revisions)
 Revision as of 20:11, 2 April 2013 (view source) (answered 4 questions where p<0.05)← Previous diff Revision as of 20:14, 2 April 2013 (view source) (→ZAP1: put spaces between < and numbers)Next diff → Line 3: Line 3: *Each time point had 4 replicates. *Each time point had 4 replicates. *The dollar sign is important because the formulas must include the same average and same standard deviation when they are pasted down the entire column. WIthout the use of the dollar sign the excel would continue to down the column and use the wrong cells in the formula. *The dollar sign is important because the formulas must include the same average and same standard deviation when they are pasted down the entire column. WIthout the use of the dollar sign the excel would continue to down the column and use the wrong cells in the formula. - *Genes with p value <0.05 + *Genes with p value < 0.05 **t15: 771 **t15: 771 **t30: 1150 **t30: 1150 Line 9: Line 9: **t90: 364 **t90: 364 **t120: 375 **t120: 375 - *Genes with p value <0.01 + *Genes with p value < 0.01 **t15: 189 **t15: 189 **t30: 340 **t30: 340 Line 15: Line 15: **t90: 73 **t90: 73 **t120: 75 **t120: 75 - *Genes with p value <0.001 + *Genes with p value < 0.001 **t15: 20 **t15: 20 **t30: 35 **t30: 35 Line 21: Line 21: **t90: 7 **t90: 7 **t120: 3 **t120: 3 - *Genes with p value <0.0001 + *Genes with p value < 0.0001 **t15: 4 **t15: 4 **t30: 6 **t30: 6 Line 27: Line 27: **t90: 0 **t90: 0 **t120: 0 **t120: 0 - *Genes still significantly changed at p <0.05 after Bonferroni correction + *Genes still significantly changed at p < 0.05 after Bonferroni correction **t15: 1 **t15: 1 **t30: 2 **t30: 2

## Microarray Data Analysis

### ZAP1

• Each time point had 4 replicates.
• The dollar sign is important because the formulas must include the same average and same standard deviation when they are pasted down the entire column. WIthout the use of the dollar sign the excel would continue to down the column and use the wrong cells in the formula.
• Genes with p value < 0.05
• t15: 771
• t30: 1150
• t60: 1610
• t90: 364
• t120: 375
• Genes with p value < 0.01
• t15: 189
• t30: 340
• t60: 592
• t90: 73
• t120: 75
• Genes with p value < 0.001
• t15: 20
• t30: 35
• t60: 80
• t90: 7
• t120: 3
• Genes with p value < 0.0001
• t15: 4
• t30: 6
• t60: 8
• t90: 0
• t120: 0
• Genes still significantly changed at p < 0.05 after Bonferroni correction
• t15: 1
• t30: 2
• t60: 0
• t90: 0
• t120: 0
• Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria? (time = t60)
• 786
• Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria? (time = t60)
• 824
• Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05? (time = t60)
• 755
• How many have an average log fold change of < -0.25 and p < 0.05? (time = t60)
• 763