SUPPORT / SAMPLES & SAS NOTES
Problem Note 17646: PROC ALLLELE reports incorrect statistics with HAPLO=NONEHWD if individuals have missing alleles
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The correlation coefficient and chi-square goodness-of-fit test used to test markers for Hardy-Weinberg Equilibrium (HWE) are incorrectly computed in PROC ALLELE when the HAPLO=NONEHWD option is specified on the proc statement and individuals have missing alleles present.
When HAPLO=NONEHWD, the HWE coefficients that are used in the denominator of the correlation coefficient and chi-square test should be calculated using only individuals that are genotyped at both markers in the pair. Currently, all individuals genotyped at the single marker are being used.
There is no circumvention for this problem.
Select the Hot Fix tab in this note to access the hot fix for this issue.
Operating System and Release Information
| Product Family | Product | System | Product Release | SAS Release | ||
| Reported | Fixed* | Reported | Fixed* | |||
| SAS System | SAS/Genetics | Microsoft Windows XP 64-bit Edition | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 |
| Microsoft Windows NT Workstation | 2.2 | 9.1 TS1M3 | ||||
| Microsoft Windows XP Professional | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| Microsoft® Windows® for 64-Bit Itanium-based Systems | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| Microsoft Windows Server 2003 Enterprise Edition | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| Microsoft Windows Server 2003 Standard Edition | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| Microsoft Windows 2000 Server | 2.2 | 9.1 TS1M3 | ||||
| Microsoft Windows Server 2003 Datacenter Edition | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| Microsoft Windows 2000 Advanced Server | 2.2 | 9.1 TS1M3 | ||||
| Microsoft Windows 2000 Datacenter Server | 2.2 | 9.1 TS1M3 | ||||
| Microsoft Windows 2000 Professional | 2.2 | 9.1 TS1M3 | ||||
| 64-bit Enabled Solaris | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| z/OS | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| Linux | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| 64-bit Enabled HP-UX | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| Linux on Itanium | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| HP-UX IPF | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| OpenVMS Alpha | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| 64-bit Enabled AIX | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||
| Tru64 UNIX | 2.2 | 2.2 | 9.1 TS1M3 | 9.2 TS1M0 | ||