I have some additional questions, after having run this program.
1) when I specify the error term as mvlr, I always get an error saying matrix is singular. I tried changing the error term to uvlr, and that solves the problem. However, I believe I really should be using the mvlr, because in all my tissues I have the exact same individuals.
Run (I shortened filenames for clarity):
cmd-line: lt-eqtlbma_bf --geno _geno_chr21 --exp exp_chr21 --scoord 21_snppos.bed.gz --gcoord expTSS.bed --anchor TSS --cis 1000000 --out chr21 --type join --gridL grid_phi2_oma2_general.txt.gz --gridS grid_phi2_oma2_with-configs.txt.gz --bfs all --error mvlr --qnorm
Error reproduced here:
total nb of SNPs to analyze: 122816
load grid in /srv/gs1/projects/snyder/jzaugg/histoneQTL/jointQTL/data/grid_phi2_oma2_general.txt.gz ...
grid size: 25
load grid in /srv/gs1/projects/snyder/jzaugg/histoneQTL/jointQTL/data/grid_phi2_oma2_with-configs.txt.gz ...
grid size: 10
look for association between each pair gene-SNP ...
likelihood=normal errors=mvlr prop_cov_errors=0.50 anchor=TSS radius=1000000
=========================================== 86.22%gsl: lu.c:262: ERROR: matrix is singular
Default GSL error handler invoked.
Aborted
2) when I run eqtlbma_bf, i get nan for some values on the grid, and some rows. Is that normal, or does that indicate an error?
Run: same as above but with uvlr
Here is an example:
gene snp config l10abf.grid1 l10abf.grid2 l10abf.grid3 l10abf.grid4 l10abf.grid5 l10abf.grid6 l10abf.grid7 l10abf.grid8 l10abf.grid9 l10abf.grid10 l10abf.grid11 l10abf.grid12 l10abf.grid13 l10abf.grid14 l10abf.grid15 l10abf.grid16 l10abf.grid17 l10abf.grid18 l10abf.grid19 l10abf.grid20 l10abf.grid21 l10abf.grid22 l10abf.grid23 l10abf.grid24 l10abf.grid25
g1 rs74700993 gen 3.010325e-02 6.667264e-02 1.008149e-01 1.328496e-01 1.630494e-01 7.337196e-02 1.597779e-01 2.327912e-01 2.974713e-01 3.572021e-01 1.822143e-02 1.187750e-01 2.098473e-01 3.090112e-01 4.317469e-01 -3.918792e-01 -3.247306e-01 -2.239222e-01-5.721876e-02 2.875899e-01 -1.117384e+00 -1.071324e+00 -9.621280e-01 -7.397135e-01 3.290463e-02
g1 rs74700993 gen-fix 1.630494e-01 1.630494e-01 1.630494e-01 1.630494e-01 1.630494e-01 3.572021e-01 3.572021e-01 3.572021e-01 3.572021e-01 3.572021e-01 4.317469e-01 4.317469e-01 4.317469e-01 4.317469e-01 4.317469e-01 2.875899e-01 2.875899e-01 2.875899e-01 2.875899e-01 2.875899e-01 3.290463e-02 3.290463e-02 3.290463e-02 3.290463e-02 3.290463e-02
g1 rs74700993 gen-maxh 3.010325e-02 3.010325e-02 3.010325e-02 3.010325e-02 3.010325e-02 7.337196e-02 7.337196e-02 7.337196e-02 7.337196e-02 7.337196e-02 1.822143e-02 1.822143e-02 1.822143e-02 1.822143e-02 1.822143e-02 -3.918792e-01 -3.918792e-01 -3.918792e-01 -3.918792e-01 -3.918792e-01 -1.117384e+00 -1.117384e+00 -1.117384e+00 -1.117384e+00 -1.117384e+00
g1 rs74700993 1 2.033034e-02 2.033034e-02 5.713568e-02 5.713568e-02 7.765497e-02 7.765497e-02 -2.871425e-02-2.871425e-02 -2.584742e-01 -2.584742e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 2 -6.194595e-03 -6.194595e-03 -2.705216e-02 -2.705216e-02 -1.067565e-01 -1.067565e-01 -2.912661e-01-2.912661e-01 -5.521341e-01 -5.521341e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 3 1.596751e-02 1.596751e-02 4.328844e-02 4.328844e-02 4.732293e-02 4.732293e-02 -7.189885e-02-7.189885e-02 -3.067755e-01 -3.067755e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 1-2 4.465814e-02 5.430667e-02 1.034399e-01 1.262786e-01 7.861843e-02 1.307712e-01 -1.820693e-01-2.673854e-02 -6.462906e-01 -2.828212e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 1-3 8.582202e-02 1.014462e-01 2.179070e-01 2.537697e-01 2.822355e-01 3.529339e-01 6.380535e-02 2.460691e-01 -3.920003e-01 6.473547e-03 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 2-3 3.869692e-02 4.789267e-02 8.651767e-02 1.089317e-01 4.663703e-02 1.005428e-01 -2.248914e-01-6.385790e-02 -6.942270e-01 -3.221839e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
Hi,
Thank you very much for all your help.
I have some additional questions, after having run this program.
1) when I specify the error term as mvlr, I always get an error saying matrix is singular. I tried changing the error term to uvlr, and that solves the problem. However, I believe I really should be using the mvlr, because in all my tissues I have the exact same individuals.
Run (I shortened filenames for clarity): cmd-line: lt-eqtlbma_bf --geno _geno_chr21 --exp exp_chr21 --scoord 21_snppos.bed.gz --gcoord expTSS.bed --anchor TSS --cis 1000000 --out chr21 --type join --gridL grid_phi2_oma2_general.txt.gz --gridS grid_phi2_oma2_with-configs.txt.gz --bfs all --error mvlr --qnorm
Error reproduced here: total nb of SNPs to analyze: 122816 load grid in /srv/gs1/projects/snyder/jzaugg/histoneQTL/jointQTL/data/grid_phi2_oma2_general.txt.gz ... grid size: 25 load grid in /srv/gs1/projects/snyder/jzaugg/histoneQTL/jointQTL/data/grid_phi2_oma2_with-configs.txt.gz ... grid size: 10 look for association between each pair gene-SNP ... likelihood=normal errors=mvlr prop_cov_errors=0.50 anchor=TSS radius=1000000 =========================================== 86.22%gsl: lu.c:262: ERROR: matrix is singular Default GSL error handler invoked. Aborted
2) when I run eqtlbma_bf, i get nan for some values on the grid, and some rows. Is that normal, or does that indicate an error?
Run: same as above but with uvlr
Here is an example: gene snp config l10abf.grid1 l10abf.grid2 l10abf.grid3 l10abf.grid4 l10abf.grid5 l10abf.grid6 l10abf.grid7 l10abf.grid8 l10abf.grid9 l10abf.grid10 l10abf.grid11 l10abf.grid12 l10abf.grid13 l10abf.grid14 l10abf.grid15 l10abf.grid16 l10abf.grid17 l10abf.grid18 l10abf.grid19 l10abf.grid20 l10abf.grid21 l10abf.grid22 l10abf.grid23 l10abf.grid24 l10abf.grid25 g1 rs74700993 gen 3.010325e-02 6.667264e-02 1.008149e-01 1.328496e-01 1.630494e-01 7.337196e-02 1.597779e-01 2.327912e-01 2.974713e-01 3.572021e-01 1.822143e-02 1.187750e-01 2.098473e-01 3.090112e-01 4.317469e-01 -3.918792e-01 -3.247306e-01 -2.239222e-01-5.721876e-02 2.875899e-01 -1.117384e+00 -1.071324e+00 -9.621280e-01 -7.397135e-01 3.290463e-02 g1 rs74700993 gen-fix 1.630494e-01 1.630494e-01 1.630494e-01 1.630494e-01 1.630494e-01 3.572021e-01 3.572021e-01 3.572021e-01 3.572021e-01 3.572021e-01 4.317469e-01 4.317469e-01 4.317469e-01 4.317469e-01 4.317469e-01 2.875899e-01 2.875899e-01 2.875899e-01 2.875899e-01 2.875899e-01 3.290463e-02 3.290463e-02 3.290463e-02 3.290463e-02 3.290463e-02 g1 rs74700993 gen-maxh 3.010325e-02 3.010325e-02 3.010325e-02 3.010325e-02 3.010325e-02 7.337196e-02 7.337196e-02 7.337196e-02 7.337196e-02 7.337196e-02 1.822143e-02 1.822143e-02 1.822143e-02 1.822143e-02 1.822143e-02 -3.918792e-01 -3.918792e-01 -3.918792e-01 -3.918792e-01 -3.918792e-01 -1.117384e+00 -1.117384e+00 -1.117384e+00 -1.117384e+00 -1.117384e+00 g1 rs74700993 1 2.033034e-02 2.033034e-02 5.713568e-02 5.713568e-02 7.765497e-02 7.765497e-02 -2.871425e-02-2.871425e-02 -2.584742e-01 -2.584742e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan g1 rs74700993 2 -6.194595e-03 -6.194595e-03 -2.705216e-02 -2.705216e-02 -1.067565e-01 -1.067565e-01 -2.912661e-01-2.912661e-01 -5.521341e-01 -5.521341e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan g1 rs74700993 3 1.596751e-02 1.596751e-02 4.328844e-02 4.328844e-02 4.732293e-02 4.732293e-02 -7.189885e-02-7.189885e-02 -3.067755e-01 -3.067755e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan g1 rs74700993 1-2 4.465814e-02 5.430667e-02 1.034399e-01 1.262786e-01 7.861843e-02 1.307712e-01 -1.820693e-01-2.673854e-02 -6.462906e-01 -2.828212e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan g1 rs74700993 1-3 8.582202e-02 1.014462e-01 2.179070e-01 2.537697e-01 2.822355e-01 3.529339e-01 6.380535e-02 2.460691e-01 -3.920003e-01 6.473547e-03 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan g1 rs74700993 2-3 3.869692e-02 4.789267e-02 8.651767e-02 1.089317e-01 4.663703e-02 1.005428e-01 -2.248914e-01-6.385790e-02 -6.942270e-01 -3.221839e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
Thank you very much, Oana