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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).

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).

2 REPLIES
dougr

Staff

Joined:

Oct 2, 2013

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

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).

reply from Doug Robinson<https://community.jmp.com/people/dougR?et=watches.email.thread> in Discussions - View the full discussion<https://community.jmp.com/message/213359?et=watches.email.thread#213359>