I'm a new Probabel user attempting to trial this software for an upcoming GWAS. During the run, every SNP seems to have a matrix error:

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`Warning for rs724512: X matrix deemed to be singular (variable 2)`

Warning for rs1188382: X matrix deemed to be singular (variable 2)

Warning for rs1188383: X matrix deemed to be singular (variable 2)

Warning for rs1188384: X matrix deemed to be singular (variable 2)

Warning for rs111627626: X matrix deemed to be singular (variable 2)

Warning for rs113280400: X matrix deemed to be singular (variable 2)

Warning for rs1188385: X matrix deemed to be singular (variable 2)

Warning for rs77506101: X matrix deemed to be singular (variable 2)

Warning for rs2147081: nr of iterations >= MAXITER (20): 20

Warning for rs2147081: Cox regression ran out of iterations and did not converge, setting beta and se to 'NaN'

Warning for rs1188386: X matrix deemed to be singular (variable 2)

Warning for rs79951922: X matrix deemed to be singular (variable 2)

Warning for rs76912545: X matrix deemed to be singular (variable 2)

Warning for rs1188387: X matrix deemed to be singular (variable 2)

Warning for 131149813TCT: X matrix deemed to be singular (variable 2)

Warning for rs1188388: X matrix deemed to be singular (variable 2)

Warning for rs1188389: X matrix deemed to be singular (variable 2)

Warning for rs75262501: X matrix deemed to be singular (variable 2)

Warning for rs78715304: X matrix deemed to be singular (variable 2)

Warning for rs1920423: X matrix deemed to be singular (variable 2)

Warning for rs2700541: X matrix deemed to be singular (variable 2)

Warning for rs1408151: X matrix deemed to be singular (variable 2)

Warning for rs1188390: X matrix deemed to be singular (variable 2)

The first 5 lines of my info:

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`#SNP Al1 Al2 Freq1 MAF Quality Rsq`

rs116559375 A G 30028088 0.5 0.9 0.9

rs116379285 C T 30028139 0.5 0.9 0.9

rs116095946 T C 30028141 0.5 0.9 0.9

rs74066615 T C 30028236 0.5 0.9 0.9

rs72652657 C G 30028329 0.5 0.9 0.9

rs67913534 T C 30028437 0.5 0.9 0.9

rs28742271 T C 30028717 0.5 0.9 0.9

rs28588071 G A 30028730 0.5 0.9 0.9

rs78986157 T C 30028825 0.5 0.9 0.9

(With final three columns arbitrarily set as this info was not provided in our original dosage files)

Dose file:

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`TOR1201-04 MLDOSE 0.331 0.327 0.064 0.139 0.081 1.533 0.328 1.191`

TOR1203-03 MLDOSE 0.765 0.766 0.14 0.196 0.213 1.038 0.765 0.069

TOR1216-03 MLDOSE 0.855 0.855 0.368 0.406 0.268 0.738 0.857 0.109

TOR1228-03 MLDOSE 0.183 0.183 0.013 0.02 1.738 1.797 0.183 0.028

TOR1244-03 MLDOSE 0.871 0.869 0.105 0.27 0.224 0.86 0.869 0.249

TOR1255-03 MLDOSE 1.192 1.191 0.05 0.112 0.161 0.697 1.194 0.111

TOR1261-03 MLDOSE 1.091 1.091 0.145 0.163 0.038 0.746 1.091 0.6

TOR1261-04 MLDOSE 0.411 0.405 0.093 0.17 0.342 1.427 0.403 0.863

TOR1265-03 MLDOSE 0.91 0.91 0.01 0.015 0.009 1.074 0.911 0.041

TOR1265-04 MLDOSE 0.636 0.636 0.134 0.155 0.68 1.21 0.634 0.297

Pheno file:

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`id fupt_chd chd arbitrarycov`

TOR1201-04 9.9150684932 0 1

TOR1203-03 11.860273973 0 1

TOR1216-03 9.2712328767 0 1

TOR1228-03 14.043835616 0 1

TOR1244-03 11.010958904 0 1

TOR1255-03 11.068493151 0 1

TOR1261-03 12.830136986 0 1

TOR1261-04 10.8 0 1

TOR1265-03 10.052054795 0 1

(Had to add last column -fake covariate- to achieve run)

In total, I have ~40,000 snps and ~300 samples in this dataset.

Any suggestions? I apologize if I could not find the answer in previous posts.