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Phenotype file and dose or probability file did not match at line

Posted: Thu Oct 19, 2017 5:28 pm
by msarguru
Hello all,

I guess this is a known bug, that throws when running either the palinear or palogisitc. I tried to compare the phenotype file and genotype file, the sampleID matches well (ID in phenotype file same as genotypefile (line number -1) taking the header in the phenotype file in to account)

line sampleID phenotypevalue covariables1 covariables2 covariables3 covariables4 covariables5 covariables6
15 840_840 NA NA NA NA NA NA NA
16 832_832 NA NA 0 NA 0.0052 0.0166
17 824_824 NA NA 1 NA 0.0249
18 808_808 0 71.50992 1 1522.44 0.0062 0.0057
19 800_800 NA NA 1 NA 0.0072
20 784_784 NA NA 0 NA 0.024 0.0435 0.01
21 864_864 0 69.68925 0 1581.066 0.0313 0.0153

Reading genotype data... phenotype file and dose or probability file did not match at line 18 (0.000 != 808_808)

I believe this has got nothing to do with the models
As everytime when I change the phenotype value to NA, the error moves to the next line with non NA values
For example when I change the phenotypevalue at line 18 to NA, the following error throws up..
Reading genotype data... phenotype file and dose or probability file did not match at line 21 (0.000 != 864_864)

I am running the following version
probabel/0.4.4
I guess there should not be a problem with the version, as it was running smoothly with other genotype files.

Any suggestions will be of great help.
Thanks
Murali