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statgen / METAL

Meta-analysis of genomewide association scans
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Hi, about the STDERR/EFFECT_PRINT_PERCISION #36

Open seisland1 opened 11 months ago

seisland1 commented 11 months ago

Hi, statgen :)

I did run below command lines : SEPARATOR TAB/MARKER SNP/ALLELE E NE/EFFECT BETA/PVALUE P/DEFAULTWEIGHT 7639/FREQLABEL FREQ/ PROCESS Meta_CAVAS_entire.txt

SEPARATOR TAB/MARKER SNP/ALLELE E NE/EFFECT BETA/PVALUE P/DEFAULTWEIGHT 4601/FREQLABEL FREQ/ PROCESS Meta_KARE_entire.txt

EFFECT_PRINT_PRECISION 3 STDERR_PRINT_PRECISION 3 AVERAGEFREQ ON OUTFILE Entire_beta.tbl ANALYZE

QUIT

but I got error message like : Processing file 'Meta_KARE_entire.txt' WARNING: No 'N' column found -- using DEFAULTWEIGHT = 4601 Processed 40 markers ...

Set print pecision for Effect to 3 ... Set print pecision for StdErr to 3 ... ERROR: Meta-analysis in progress - before issuing this command, use CLEAR command ERROR: The command you issued could not be processed ...

Executing meta-analysis ... Complete results will be stored in file 'METAANALYSIS1.TBL' Column descriptions will be stored in file 'METAANALYSIS1.TBL.info' Completed meta-analysis for 48 markers! Smallest p-value is 3.49e-216 at marker 'rs651821'

Can you kindly help me about this issue? I really appreciate your program.

I lookforward to your answer

Sincerely,

Sei Kim

seisland1 commented 11 months ago

Also, my results file name is not what I set. And this is the result files' header "MarkerName Allele1 Allele2 Weight Zscore P-value Direction"

I wanna get effect and SE from result. :)

Thank you