Question: SNPTEST:number of samples below limit
gravatar for krishnapashu912
3.0 years ago by
krishnapashu91220 wrote:


I have recently started doing GWAS and I chose to do it with SNPTEST. I would appreciate if you could help me with the following question,

I have 2500 samples. I have two phenotypes of interest - continuous (0 - 1.5) and discrete phenotype (numbers between 0 to 20). There are 500 missing values and 400 zeros in the continuous phenotype.

My questions are as follows,

  1. SNPTEST with the continuous phenotype gives output file that has no P-values at all. It says "number of samples below limit". Is it due to the missing values and zeros. I still have more than 1000 samples, is it too low for a good fit?

  2. I am not able to run SNPTEST with discrete phenotype (numbers between 0 to 20). I get error that "this is not one of the phenotypes in the sample files". However I checked and its there in the file categorized as Discrete (D). Does the positioning of the phenotype variables matter in the phenotype file?

I would appreciate for any help here!

best regards, Krishna

snptest gwas • 1.1k views
ADD COMMENTlink written 3.0 years ago by krishnapashu91220
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1795 users visited in the last hour