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s_wimmers

Community Trekker

Joined:

Oct 12, 2014

Why JMP genomics calculation of only 20000 markers instead of 40000 markers by ordinal traits with random, fix and covariance effect (Proc Grimmix).

Why JMP genomics calculation of only 20000 markers instead of 40000 markers by ordinal traits with random, fix and covariance effect (Proc Grimmix).

2 REPLIES
dougr

Staff (Retired)

Joined:

Oct 2, 2013

Re: Why JMP genomics calculation of only 20000 markers instead of 40000 markers by ordinal traits with random, fix and covariance effect (Proc Grimmix).

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.

s_wimmers

Community Trekker

Joined:

Oct 12, 2014

Re: 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).

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Why JMP genomics calculation of only 20000 markers instead of 40000 markers by ordinal traits with random, fix and covariance effect (Proc Grimmix).

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