<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />Why JMP genomics calculation of only 20000 markers instead of 40000 markers by ordinal traits with random, fix and covariance effect (Proc Grimmix).
Dear Doug
Thank for fast response. I think my settings file are OK. I send you some SAS log file which calculation of only 30000 markers instead of 48909 markers of 300 samples. I think it can be the problem of not enough memory in my computer.
Can I use JMP genomic from my computer and SAS from other bigger servers.
Here for example of some cut of log file.
NOTE: There were 48909 observations read from the data set WORK.TEMP1.
NOTE: The data set WORK.TEMP has 48909 observations and 3 variables.
NOTE: PROCEDURE PSMOOTH used (Total process time):
real time 0.03 seconds
cpu time 0.04 seconds
WARNING: Argument 2 to macro function %SUBSTR is out of range.
WARNING: Argument 3 to macro function %SUBSTR is out of range.
NOTE: There were 48909 observations read from the data set WORK.TEMP1.
NOTE: There were 48909 observations read from the data set WORK.TEMP.
NOTE: The data set OUTLIB.WT5_26_DMG_IBD_KC_QKM has 48909 observations and 29 variables.
NOTE: DATA statement used (Total process time):
real time 0.04 seconds
cpu time 0.04 seconds
WARNING: An argument to the function LOG10 referenced by the %SYSFUNC or %QSYSFUNC macro function
is out of range.
NOTE: Mathematical operations could not be performed during %SYSFUNC function execution. The
result of the operations have been set to a missing value.
NOTE: Missing values were generated as a result of performing an operation on missing values
during %SYSEVALF expression evaluation.
NOTE: There were 48909 observations read from the data set OUTLIB.WT5_26_DMG_IBD_KC_QKM.
NOTE: The data set OUTLIB.WT5_26_DMG_IBD_KC_QKM has 48909 observations and 28 variables.
NOTE: DATA statement used (Total process time):
real time 0.03 seconds
cpu time 0.03 seconds
Best,
Siriluck
Von: dougR
Gesendet: Monday, October 13, 2014 4:38 PM
An: Wimmers, Siriluck
Betreff: Re: - Why JMP genomics calculation of only 20000 markers instead of 40000 markers by ordinal traits with random, fix and covariance effect (Proc Grimmix).
JMP User Community<>
Why JMP genomics calculation of only 20000 markers instead of 40000 markers by ordinal traits with random, fix and covariance effect (Proc Grimmix).
reply from Doug Robinson<> in Discussions - View the full discussion<>
I think we need a bit more information about this. Were there any errors? Our initial guess is the the type of marker was checked as "Allelic" when in fact it is either genotype or a non-delimited genotype (both alleles represented in a single column for each marker in the data table). If you could send the settings file, that would help.
