Phenotype format in case of having multiple samples associated with each genotype

[Shadi Nayeri]

Hello,

I am running eQTL analysis using GEMMA. I have 150 individuals (genotypes) and my expression data is 280 samples, some individuals with 3 biopsy samples from three different locations. So it means that I have more than one sample for each individual (genotype).

I was looking at the manual and based on the manual each row (ID) in my expression (phenotype data) file should have a corresponding ID in the genotype. How does GEMMA handle cases like this in the analysis where there are more samples in the dataset for each genotype ID? and how should I make my phenotype file?

I appreciate your insight and input in this regard,

Best,

SN

Example of my expression data:

sample ID  genotype ID.   gene1.   gene2

370_1         1605.              0.4.         0.5

390_2.        1605.              4              1

400_3.        1043               0.5           0.2

405_3         1002              0.3.           0.5

100_2.        1043.             0.6           0.3

example of genotype data

genotype ID. SNP1 SNP2 SNP3 ... etc

1605

1043

1002

[Jeremy Sutherland]

Did you get an answer to this question? I have a similar situation.