Question: Association Analysis with Plink error
1
gravatar for mmukhame321
3.5 years ago by
mmukhame32130
United States
mmukhame32130 wrote:

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 association plink2 • 3.1k views
ADD COMMENTlink modified 12 months ago by zx87548.2k • written 3.5 years ago by mmukhame32130

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

ADD REPLYlink written 3.5 years ago by Philipp Bayer6.5k
2
gravatar for yulin1988320
12 months ago by
yulin198832020
yulin198832020 wrote:

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.

ADD COMMENTlink modified 12 months ago • written 12 months ago by yulin198832020

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.

ADD REPLYlink written 3 months ago by Diesel0

I have now toggled this old answer as accepted

ADD REPLYlink written 3 months ago by Kevin Blighe48k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1959 users visited in the last hour