Association Analysis with Plink error
2
4
Entering edit mode
5.8 years ago
mmukhame321 ▴ 60

1. this is my phenotype file (called outputfile.txt in command line use):

FID IID Cadmium_Chloride    Caffeine    Calcium_Chloride    Cisplatin   Cobalt_Chloride Congo_red   Copper  Cycloheximide   Diamide E6_Berbamine    Ethanol Formamide   Galactose   Hydrogen_Peroxide   Hydroquinone    Hydroxyurea Indoleacetic_Acid   Lactate Lactose Lithium_Chloride    Magnesium_Chloride  Magnesium_Sulfate   Maltose Mannose Menadione   Neomycin    Paraquat    Raffinose   SDS Sorbitol    Trehalose   Tunicamycin x4-Hydroxybenzaldehyde  x4NQO   x5-Fluorocytosine   x5-Fluorouracil x6-Azauracil    Xylose  YNB YNB:ph3 YNB:ph8 YPD YPD:15C YPD:37C YPD:4C  Zeocin
A01_01 A01_01 -7.32351970578731 0.279992827000249 0.313118165836545 1.65817907082079 -1.60444210190495 5.84161725611811 -4.13094977046224 0.821226166664529 3.62260156257758 -0.378746805086589 -0.6449544101999 0.736772421684145 1.46869950807288 4.25247880427656 -0.439429122584143 0.471260934436784 -0.502023574403563 -0.0196386553492135 -0.520403819717771 -3.04250228422253 -0.239535833991348 3.24339670861968 -3.94506679134117 2.13462934930907 2.02778180052776 -10.930132784538 1.5331378908103 -0.768634428150619 0.718639222878471 NA -0.734761808299035 0.760529220008652 -0.756192366531865 2.09460844047308 0.20839083641332 1.39503843403223 1.19905393883646 -0.309148758204671 17.470821887375 0.055225386257017 -0.184268373327551 24.5489707854467 0.712171057826513 0.890841948461777 4.11837231021474 8.59281835912838
A01_02 A01_02 -8.09823582391425 -0.206326076018097 -0.534843782803465 -0.918011723216776 0.892197592923579 -1.61817232545715 1.13194737114694 -0.764735687307454 -2.94627867266571 -2.47519275599105 -0.203037737638922 -0.661085887535845 1.74459605348331 -3.83556423753907 -0.120208249207331 -1.99993926169807 -1.09816332010706 0.649474778852619 -0.586994384784721 2.64012099474669 -0.308361579587721 -1.14413156235224 -5.39735154446785 0.319899854554594 -1.72754411262877 5.08769611065373 -0.691267578117329 2.46423743955996 -0.706985029180143 NA -0.3904578652155 -0.598586077448249 2.3069619915968 -3.57657131625641 -0.53930290771097 0.631594704977842 0.44318172585355 0.697908024887215 18.0529250220805 0.28346211824195 1.66220146506514 26.808475766906 -1.52249804709209 0.0060616411700553 0.0665150029109814 -4.22047646027812

2. I would like to perform quantitative association testing for all traits. I have been fighting all day and cant find an answer anymore, why I am getting an error (see below), when running this command line:

$ plink2 --assoc --bfile binary_fileset --pheno outputfile.txt --pheno-name Caffeine -pfilter 1e-5

Error:

4096 MB RAM detected; reserving 2048 MB for main workspace.
11623 variants loaded from .bim file.
1008 people (0 males, 0 females, 1008 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
0 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1008 founders and 0 nonfounders present.
Calculating allele frequencies... done.
11623 variants and 1008 people pass filters and QC.
Note: No phenotypes present.
Warning: Skipping --assoc/--model since less than two phenotypes are present.
SNP plink plink2 association • 7.7k views
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Have you tried running it with --all-pheno instead of --pheno-name Caffeine? Maybe it doesn't properly pick up the caffeine phenotype for some weird reason

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6
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3.4 years ago
yulin1988320 ▴ 60

Hi mmukhame321, I guess you have solved this problem. It took me a while to find out why. My .fam file does not include the gender information, so there will be a warning like "If you don't want those phenotypes to be ignored, use the --allow-no-sex flag". I suppose that's why it came out to the "Note: No phenotypes present." After I added the flag "--allow-no-sex", it worked. Hope this information could help others who are disturbed by this annoying problem.

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Many many thanks for this. I was about to waste my full day (already 2 hours wasted) trying to understand why it was not working. It is indeed true, if the .fam does not include gender information you need to use the --allow-no-sex flag else phenotypes will be ignored.

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1
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I have now toggled this old answer as accepted

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17 months ago
fanqianyin • 0

For my experience, the problem could be: The family ID and individual ID in your phenotype file does not match these columns in the .fam file. For example, one individual in .fam with:

head -1 yourfile.fam #view first row of the file

#FID IID phenotype1 (actually, .fam file may not contain this title row; and here I just show first three columns.)
0 individual1 2

but the same individual in .pheno (phenotype file) with:

head -2 yourfile.pheno #view first  two rows of the file

FID IID phenotype1
individual1 individual1 2

The solution is to replace "individual1" in FID column with "0" in your phenotype file, result in:

head -2 yourfile.pheno #view first  two rows of the file

FID IID phenotype1
0 individual1 2

(Note: if you use the title in the first row, i.e. "FID IID phenotype1" as above, do not forget to use flag --pheno-name phenotype1.)

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