Problem Note 40534: The ALLELE procedure incorrectly reports LD Coeff, Corr Coeff, and haplotype frequencies
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The Linkage Disequilibrium Measures table in PROC ALLELE incorrectly reports the haplotype frequencies, LD coefficient, and LD measures when one allele for a marker only occurs in individuals with a missing genotype at the other marker in the pair. The LD coefficient should be zero and the LD measures should be missing. The haplotype frequencies for this pair are incorrect.
There is no circumvention for this problem.
Click the Hot Fix tab in this note to access the hot fix for this issue.
Operating System and Release Information
| Product Family | Product | System | SAS Release | |
| Reported | Fixed* | |||
| SAS System | SAS/Genetics | z/OS | 9.2 TS1M0 | 9.3 TS1M0 |
| Microsoft® Windows® for 64-Bit Itanium-based Systems | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Microsoft Windows Server 2003 Datacenter 64-bit Edition | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Microsoft Windows Server 2003 Enterprise 64-bit Edition | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Microsoft Windows XP 64-bit Edition | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Microsoft® Windows® for x64 | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Microsoft Windows Server 2003 Datacenter Edition | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Microsoft Windows Server 2003 Enterprise Edition | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Microsoft Windows Server 2003 Standard Edition | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Microsoft Windows XP Professional | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Windows Vista | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Windows Vista for x64 | 9.2 TS1M0 | 9.3 TS1M0 | ||
| 64-bit Enabled AIX | 9.2 TS1M0 | 9.3 TS1M0 | ||
| 64-bit Enabled HP-UX | 9.2 TS1M0 | 9.3 TS1M0 | ||
| 64-bit Enabled Solaris | 9.2 TS1M0 | 9.3 TS1M0 | ||
| HP-UX IPF | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Linux | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Linux for x64 | 9.2 TS1M0 | 9.3 TS1M0 | ||
| OpenVMS on HP Integrity | 9.2 TS1M0 | 9.3 TS1M0 | ||
| Solaris for x64 | 9.2 TS1M0 | 9.3 TS1M0 | ||
A fix for this issue for SAS/Genetics 9.21_M2 is available at:
http://ftp.sas.com/techsup/download/hotfix/HF2/C35.html#40534| Type: | Problem Note |
| Priority: | alert |
| Topic: | Analytics ==> Genetics |
| Date Modified: | 2010-08-10 13:11:34 |
| Date Created: | 2010-08-06 09:39:23 |