Fatal Error : SnpPairs only implemented in runGWAS_woodbury() which requires eigen->n[356] > eigen->rankU[356].

Hi, when I am trying to run FaSTLMM v2.07 on Unbuntu system with command: fastlmmc -snpPairs -file cleanF2deChr0 -fileSim cleanF2deChr0 -extractSim foodfrequency.snps.txt -pheno test_phe.txt -p...

Id #21573 | Release: None | Updated: Nov 21, 2014 at 6:35 PM by heckerma | Created: Nov 20, 2014 at 10:02 AM by fengzhang

missing output files with feature_selection_cv.py for UNIX

Hello; I run feature_selection_cv.py for UNIX and I've got only the _mse.txt file. The other files, especially the most significant - _report.txt and _snps.cnv - are missing. The Log reports a weal...

Id #21262 | Release: None | Updated: Aug 28, 2014 at 8:07 AM by PDubreuil | Created: Aug 28, 2014 at 8:07 AM by PDubreuil

Re-use decomposition object

Hello, I have a question concerning the re-use of the decomposition object. My dataset contains 22.500 phenotypes and 60.000 SNPs for 200 samples. First I compute the spectral decomposition objec...

Id #21195 | Release: None | Updated: Aug 1, 2014 at 9:43 AM by fkreuchw | Created: Jul 31, 2014 at 3:43 PM by fkreuchw

Incorrect ID key mapping with -sim command

Seems like issue 17541 still isn't completly resolved in version 1.09 for Windows.   I use this command to read in a created sim-file: fastlmmc -bfile data.fastlmm -pheno data.pheno -sim data.sim ...

Id #18361 | Release: None | Updated: Nov 25, 2013 at 7:15 AM by bobd00 | Created: Jul 13, 2012 at 11:06 AM by cbss

OR and 95%CI

it would be great to have the odds ratios with 95%-confidence intervals corresponding to the p-values in the FaSTLMM output.

Id #18098 | Release: None | Updated: Feb 13, 2013 at 11:40 PM by costin_leu | Created: May 21, 2012 at 2:48 PM by costin_leu

Use of rand() rather than a better Random Number Generator (RNG)

Can we also chat about how the random numbers are being generated sometime. I saw rand() in the codebase and that kinda of scared me if we are trying to get statistically uncorrelated results at 1...

Id #17987 | Release: None | Updated: Feb 13, 2013 at 11:40 PM by bobd00 | Created: May 4, 2012 at 5:15 PM by bobd00

FastLmm continues after filtering out all SNPs as constants and fails later in MKL with a confusing message about bad parameters.

When there is a bug in my data files and 0 individuals remain after intersection, I don’t get an error about that, but instead end up getting a downstream error, a few minutes later, after being to...

Id #17876 | Release: None | Updated: Feb 13, 2013 at 11:40 PM by bobd00 | Created: Apr 18, 2012 at 12:01 AM by bobd00

Fatal Error : std=.-nan has illegal value for SNPs

I am processing dosage data of 7.8 mio imputed SNPs. Working with the Software version 1.05 i was getting this error message: Fatal Error : std=.-nan has illegal value for SNPs[:][1085]   I couldn'...

Id #17677 | Release: None | Updated: Feb 13, 2013 at 11:40 PM by costin_leu | Created: Mar 22, 2012 at 3:54 PM by costin_leu

Review obsolete usage and remove INDIVIDUAL_ID_TYPE

// obsolete? remove in future since we only support INDIVIDUAL_ONLY INDIVIDUAL_ID_TYPE individualIdType = INDIVIDUALID_ONLY;

Id #17612 | Release: None | Updated: Feb 13, 2013 at 11:40 PM by bobd00 | Created: Mar 15, 2012 at 7:29 PM by bobd00

FastLmm not parsing Mac csv files properly

I experienced the problem, when I saved a phenotype file to tab separated txt format from MS Excel on a Mac and tried running fastlmmc on Linux using that file.   Mac OS's prior to OS X used a sing...

Id #17611 | Release: None | Updated: Feb 13, 2013 at 11:40 PM by bobd00 | Created: Mar 15, 2012 at 7:24 PM by bobd00

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