Updated 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 ArticleReleased: FastLmm v1.09 Binaries for Windows and Linux (Apr 09, 2012)
------------------------------------------------------------------------------------- More current research and software can be found at the eScience FaST-LMM site:...
View ArticleUpdated Release: FastLmm v1.09 Binaries for Windows and Linux (Apr 09, 2012)
-------------------------------------------------------------------------------------More current research and software can be found at the eScience FaST-LMM...
View ArticleNew Post: -excludeByPosition
-excludeByPosition is extremely slow. Is there a workaround for this problem? Also, user manual states that 2000000 bp work well with human data, any ideas what would be sufficient for mouse data?
View ArticleNew Post: No reqults in output
will answer my own question. Your software doesn't work on large data, guys. I don't know what's the limit of number of SNPs and I don't have time to check it. Cheers
View ArticleNew Post: No reqults in output
chrustaly, Can you give a bit more on info on which version you are using and what your specific command line is. Hopefully you saw the home page pointed to a new software distribution site and are...
View ArticleNew Post: No reqults in output
Hey,I didn’t see your new site, will definitely take a look.I was running it on 2 different sets, ~400k snps x ~200 people each and got as the result all 0.Then I processed those sets with snip-snip...
View ArticleNew Post: No reqults in output
PS Probably fastlmm fails on exactly same genotype in whole column?
View ArticleNew Post: No reqults in output
I think fastlmm removes a specific SNP from consideration if there is no genotype variation in the sample set after all the individuals are selected. The best way for us to help get through or fix...
View ArticleNew Post: No reqults in output
I will run it later today and will send you the output message and everything else that I will get. I don’t remember, but hope that it will be a log file.Unfortunately I will not be able to give you my...
View ArticleNew Post: No reqults in output
Understand about the dataset. We will do our best to help figure out what is wrong in your situation too. For reporting problems, most of the output is going to stderr, so to redirect it you have to...
View ArticleCommented Issue: Incorrect ID key mapping with -sim command [18361]
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 I get...
View ArticleCommented Issue: Incorrect ID key mapping with -sim command [18361]
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 I get...
View ArticleCommented Issue: Incorrect ID key mapping with -sim command [18361]
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 I get...
View ArticleNew Post: Found missing SNP minor or major allele information in file
Hi there, I'm trying fast-lmm to run a GWAS on a quantitative trait and ran into the following error: Fatal Error : Found missing SNP minor or major allele information in file [test.bim] near line...
View ArticleNew Post: Found missing SNP minor or major allele information in file
Katie,Could you let me know what version of fastlmm are you using and what host OS? That helps me to better understand the context of any questions coming in.The PLINK docs say to encode the snp should...
View ArticleNew Post: Found missing SNP minor or major allele information in file
Hi bobd, I'm using the "FaSTLMM.207.Linux" version and running on linux platform. It would be great if you can provide some hints on how to recode the homozygous on the x or y chromosome. Thank you!
View ArticleNew Post: Found missing SNP minor or major allele information in file
Looking at the error you sent a little deeper and it indicated that the .BIM file was malformed. I was thinking this message was a specific genotype whereas a BIM file is a part of PLINK’s binary PED...
View ArticleNew Post: Found missing SNP minor or major allele information in file
Hi Bobd, It works after cleaning up those SNPs with weird coding of "0" instead of the normal "G/T/C/A". However, I'm not sure why the running of the fast-lmm got killed after the step "End Loading...
View ArticleNew Post: Found missing SNP minor or major allele information in file
Hi Katie, fastlmmc should always print an error indication if it does not complete. I'll send a private message to see about getting some data to reproduce the problem where I can debug it.
View Article