Innate Immunity in Heart, Lung and Blood Disease
Programs for Genomic Applications
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European-American Asthma 11:50 Wednesday, February 4, 2004 100
SNP = IL23A_4003
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |A |G | Total
---------+--------+--------+
Control | 4 | 906 | 910
| 0.23 | 52.49 | 52.72
---------+--------+--------+
Case | 6 | 810 | 816
| 0.35 | 46.93 | 47.28
---------+--------+--------+
Total 10 1716 1726
0.58 99.42 100.00
Frequency Missing = 26
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 0.6532 0.4190
Likelihood Ratio Chi-Square 1 0.6543 0.4186
Continuity Adj. Chi-Square 1 0.2407 0.6237
Mantel-Haenszel Chi-Square 1 0.6528 0.4191
Phi Coefficient -0.0195
Contingency Coefficient 0.0195
Cramer's V -0.0195
WARNING: 25% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 4
Left-sided Pr <= F 0.3115
Right-sided Pr >= F 0.8699
Table Probability (P) 0.1814
Two-sided Pr <= P 0.5310
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 0.5960 0.1676 2.1196
Cohort (Col1 Risk) 0.5978 0.1693 2.1109
Cohort (Col2 Risk) 1.0030 0.9957 1.0103
Effective Sample Size = 1726
Frequency Missing = 26
European-American Asthma 11:50 Wednesday, February 4, 2004 101
SNP = IL23A_4003
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |1 |3 | Total
---------+--------+--------+
Control | 2 | 453 | 455
| 0.23 | 52.49 | 52.72
---------+--------+--------+
Case | 5 | 403 | 408
| 0.58 | 46.70 | 47.28
---------+--------+--------+
Total 7 856 863
0.81 99.19 100.00
Frequency Missing = 13
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 1.6515 0.1988
Likelihood Ratio Chi-Square 1 1.6896 0.1937
Continuity Adj. Chi-Square 1 0.8191 0.3654
Mantel-Haenszel Chi-Square 1 1.6496 0.1990
Phi Coefficient -0.0437
Contingency Coefficient 0.0437
Cramer's V -0.0437
WARNING: 50% of the cells have expected counts less than 5.
(Asymptotic) Chi-Square may not be a valid test.
Pearson Chi-Square Test
----------------------------------
Chi-Square 1.6515
DF 1
Asymptotic Pr > ChiSq 0.1988
Exact Pr >= ChiSq 0.2649
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 2
Left-sided Pr <= F 0.1834
Right-sided Pr >= F 0.9542
Table Probability (P) 0.1375
Two-sided Pr <= P 0.2649
European-American Asthma 11:50 Wednesday, February 4, 2004 102
SNP = IL23A_4003
The FREQ Procedure
Statistics for Table of Allele Frequency
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 0.3558 0.0687 1.8442
Cohort (Col1 Risk) 0.3587 0.0700 1.8387
Cohort (Col2 Risk) 1.0080 0.9955 1.0205
Odds Ratio (Case-Control Study)
-----------------------------------
Odds Ratio 0.3558
Asymptotic Conf Limits
95% Lower Conf Limit 0.0687
95% Upper Conf Limit 1.8442
Exact Conf Limits
95% Lower Conf Limit 0.0337
95% Upper Conf Limit 2.1905
Effective Sample Size = 863
Frequency Missing = 13
European-American Asthma 11:50 Wednesday, February 4, 2004 103
SNP = IL23A_5870
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |A |G | Total
---------+--------+--------+
Control | 62 | 814 | 876
| 3.68 | 48.34 | 52.02
---------+--------+--------+
Case | 55 | 753 | 808
| 3.27 | 44.71 | 47.98
---------+--------+--------+
Total 117 1567 1684
6.95 93.05 100.00
Frequency Missing = 68
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 0.0476 0.8272
Likelihood Ratio Chi-Square 1 0.0477 0.8272
Continuity Adj. Chi-Square 1 0.0150 0.9026
Mantel-Haenszel Chi-Square 1 0.0476 0.8273
Phi Coefficient 0.0053
Contingency Coefficient 0.0053
Cramer's V 0.0053
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 62
Left-sided Pr <= F 0.6229
Right-sided Pr >= F 0.4518
Table Probability (P) 0.0746
Two-sided Pr <= P 0.8484
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 1.0428 0.7158 1.5193
Cohort (Col1 Risk) 1.0398 0.7325 1.4758
Cohort (Col2 Risk) 0.9971 0.9714 1.0235
Effective Sample Size = 1684
Frequency Missing = 68
European-American Asthma 11:50 Wednesday, February 4, 2004 104
SNP = IL23A_5870
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |1 |3 | Total
---------+--------+--------+
Control | 59 | 379 | 438
| 7.01 | 45.01 | 52.02
---------+--------+--------+
Case | 53 | 351 | 404
| 6.29 | 41.69 | 47.98
---------+--------+--------+
Total 112 730 842
13.30 86.70 100.00
Frequency Missing = 34
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 0.0225 0.8807
Likelihood Ratio Chi-Square 1 0.0225 0.8807
Continuity Adj. Chi-Square 1 0.0024 0.9613
Mantel-Haenszel Chi-Square 1 0.0225 0.8808
Phi Coefficient 0.0052
Contingency Coefficient 0.0052
Cramer's V 0.0052
Pearson Chi-Square Test
----------------------------------
Chi-Square 0.0225
DF 1
Asymptotic Pr > ChiSq 0.8807
Exact Pr >= ChiSq 0.9193
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 59
Left-sided Pr <= F 0.5989
Right-sided Pr >= F 0.4811
Table Probability (P) 0.0800
Two-sided Pr <= P 0.9193
European-American Asthma 11:50 Wednesday, February 4, 2004 105
SNP = IL23A_5870
The FREQ Procedure
Statistics for Table of Allele Frequency
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 1.0310 0.6922 1.5355
Cohort (Col1 Risk) 1.0268 0.7269 1.4504
Cohort (Col2 Risk) 0.9960 0.9446 1.0501
Odds Ratio (Case-Control Study)
-----------------------------------
Odds Ratio 1.0310
Asymptotic Conf Limits
95% Lower Conf Limit 0.6922
95% Upper Conf Limit 1.5355
Exact Conf Limits
95% Lower Conf Limit 0.6788
95% Upper Conf Limit 1.5687
Effective Sample Size = 842
Frequency Missing = 34