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plink linear regression

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

plink
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written by AQ7 • AQ7

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.

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written by Kevin Blighe Kevin Blighe

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
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written by AQ7 • AQ7

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
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written by Kevin Blighe Kevin Blighe

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
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written by AQ7 • AQ7

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

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written by Kevin Blighe Kevin Blighe

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. :(

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written by AQ7 • AQ7

i'm using version 1.07

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written by AQ7 • AQ7

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

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written by Kevin Blighe Kevin Blighe

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

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written by chrchang523 chrchang523

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

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written by Kevin Blighe Kevin Blighe

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

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written by AQ7 • AQ7

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

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written by AQ7 • AQ7

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