plink linear regression

Question

[AQ7]

Goodmorning everyone,

I'm trying to use plink 1.07 for a linear regression analysis with several COVs. I'm using a ped where i have cases (1) and controls (2) but when I start the analysis I get a message telling me that plink sees 0 cases and 0 controls, How is it possible? maybe for linear regression we must indicate which are cases and controls in another way? thanks a lot for you help. I attach here my command line:

plink --file mydata --linear --genotypic --covar mycovar.txt

thanks a lot

[Kevin Blighe]

good morning, information on the covariates file can be found here: https://www.cog-genomics.org/plink/1.9/input#covar

I think that the problem could be more to do with your FAM file. What are the contents of mydata.fam? You may have to create a custom FAM, depending on the source of your data.

[AQ7]

thanks a lot for you answer my fam file is like that:

id1 id1 0   0   0   1
id22    id22    0   0   0   1
id23    id23    0   0   0   1
id24    id24    0   0   0   2
id25    id25    0   0   0   2
id26    id26    0   0   0   2

[chrchang523]

You need to add --allow-no-sex to your command line, since plink 1.x throws out phenotypes of missing-sex samples by default.

[AQ7]

Sorry I've not seen your comment yestarday!!! It works adding --allow-no-sex, really thanks a lot

[Kevin Blighe]

AQ7, can you confirm that this works so that others will benefit?

[AQ7]

Yes Kevin It works!! thanks a lot for your patience and fast help

[Kevin Blighe]

Okay, FAM looks good. When you run PLINK, it is definitely using this file? - otherwise, specify it with the --fam flag.

The only other thing that I can think of is that the FID and IIDs in your genotype PED file do not exactly match those in the FAM or in mycovar.txt. The minimum information required for the covariates file is FID and IID, and then obviously a covariate of interest.

All FIDs and IIDs have to be the exact same, across:

• PED file
• FAM file
• Covariates file

[AQ7]

thanks Kevin, I've checked and yes thay are in the same order, I even try the same command line specifying --bed --fam --bim but i always get 0 cases and 0 controls output.... my covar file looks like that

id1 id1 1.838223051 0   23.42402344 0.016650571 14.98884412
id22    id22    21.25832224 0   37.92276964 0.009986684 2.536617843
id23    id23    22.41528527 0   38.83230144 0.003328673 5.981625724
id24    id24    9.410159111 0.359496705 58.1951934  0   0.692364024
id25    id25    2.416616737 0   73.21083816 0   0.276279875
id26    id26    27.49484056 0   55.18274416 0.003328673 1.208308368

[Kevin Blighe]

Which version are you using? Does it not even run as plink --file mydata --linear ?

[AQ7]

I get the same result even with just this command you suggested me. So with all NA at the end and with 0 cases and 0 controls in log file. :(

[AQ7]

i'm using version 1.07

[Kevin Blighe]

...and mydata.ped - how does that look?