association test using plink

Question

[n_09]

Hi all,

I have problem with quantitative trait association (plink).I used the following command to run this test:

./plink --file file_1 --assoc 

I am getting sample.assoc file which is not the output. output file looks something like this:

CHR                SNP         BP   A1      F_A      F_U   A2        CHISQ            P           OR
   1         rs10458597     564621    T    0.012       NA    C           NA           NA           NA
   1         rs12565286     721290    C  0.02846       NA    G           NA           NA           NA
   1         rs12082473     740857    A  0.01181       NA    G           NA           NA           NA

in place of NA there should be numerical values which is not in this case.

Thanks in advance

[cpad0112]

Could you please paste few lines from your input here?

[n_09]

input file test.map looks like this:

1    rs10458597    0    564621
1    rs12565286    0    721290
1    rs12082473    0    740857
1    rs3094315    0    752566
1    rs2286139    0    761732
1    rs2980319    0    777122
1    rs2980300    0    785989

[cpad0112]

I need few lines from test.map (already provided by you, above) and test.ped (for the snps in example map) so that I can reproduce the error. There are multiple columns with NA. Which column are you expecting to have values?

[cpad0112]

Thanks. I guess your question is addressed above.

Answer 1

[Lemire]

Bases on your output, your command is doing a basic case-control test, where the case/control status is defined in the 6th column of your ped file (taking values 0,1 or 2). In your file, the 6th column probably only contain the value 2, explaining why only F_A contains a non missing value. See this link for case/control tests:

http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#cc

You want to do a quantitative trait, make sure the 6th column contains values other than 0,1,2, or else specify a .phen file. See this link:

http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#qt

[n_09]

Thanks lemire.It worked