New Post: Detecting interaction with covariates using FaST-LMM
Hello, I was wondering whether it is possible to test gene-environment interactions with FaST-LMM. Ideally, I would like to have in the output file new columns with the p-values corresponding to the...
View ArticleNew Post: No reqults in output
Hi, I am wondering if you ever got to the bottom of this problem. I am facing the same problem now - I have input dosage files for the GWAS and have computed the genetic similarity matrix. When I use...
View ArticleCreated Unassigned: Re-use decomposition object [21195]
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 object and...
View ArticleNew Post: No reqults in output
I believe we resolved the NaN issues I was aware of. A few questions for you. Can you please confirm which version and build of fastlmm you are running and what is your host OS? And if you can send us...
View ArticleNew Post: 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 object and...
View ArticleNew Post: Re-use decomposition object
Franziska, I am not sure what your command line is specifically, but it sounds like there is a bit of confusion. The -eigenOut [directory] option produces the spectral decomposition of the similarity...
View ArticleNew Post: No reqults in output
Hi,Thank you for your reply, I am using FastLmmC v2.06.20130802 and the host OS is Linux, the starting lines of the stderr from the programme when I get it running are:FastLmmC v2.06.20130802 -...
View ArticleNew Post: Putative bug in the program feature_selection_cv.py
Hi; I get the following error message when I run feature_selection_cv.py: C:\FastLmm.Py\fastlmm\feature_selection >python feature_selection_cv.py File "feature_selection_cv.py", line33, ... from...
View ArticleCreated Unassigned: missing output files with feature_selection_cv.py for...
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 wealth of...
View ArticleNew Post: Using indicator matrix as covariates
Hi, I wonder if it is possible that using an indicator matrix for a covariates instead of the absolute values make any differences in the p-value distribution? I have two high correlated covariates:...
View ArticleUpdated Wiki: Home
More current research and software can be found at the eScience FaST-LMM site.FaST-LMM (Factored SpectrallyTransformed Linear MixedModels) is a program for performing genome-wide association studies...
View ArticleNew Post: Fatal Error : Expected phenotype indicator in file...
I am trying to use FaST-LMM the very first time, but I'm getting a following error, and I'm wondering whether the problem derives from wrong coding, or something else: FastLmmC v2.07.20131102 -...
View ArticleNew Post: Fatal Error : Expected phenotype indicator in file...
The error says fastlmmc was looking in the file allF2phe_plink.txt for a numeric value and found "foodconversion" in line 1 column 8 , so it sounds like the file is mal-formed. Do you have a header row...
View ArticleSource code checked in, #111525
Remove the files here to reduce confusion and re-direct people to FaST-LMM active development on http://github.com/MicrosoftGenomics/FaST-LMM
View ArticleUpdated Wiki: Documentation
FaST-LMM development has moved to https://github.com/MicrosoftGenomics/FaST-LMM and to minimize future confusion, we have removed the files from here. Please join us on github.
View ArticleReleased: FaST-LMM development moved (Nov 12, 2014)
FaST-LMM development has moved to https://github.com/MicrosoftGenomics/FaST-LMM and to minimize future confusion, we have removed the files from here. Please join us on github.
View ArticleUpdated Release: FaST-LMM development moved (Nov 12, 2014)
FaST-LMM development has moved to https://github.com/MicrosoftGenomics/FaST-LMM and to minimize future confusion, we have removed the files from here.Please join us on github.
View ArticleCreated Unassigned: Fatal Error : SnpPairs only implemented in...
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 -pheno-name...
View ArticleCommented Unassigned: Fatal Error : SnpPairs only implemented in...
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 -pheno-name...
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