I appreciate it if someone could direct me in this regard. I am running eQTL analysis using GEMMA software. I have corrected the expression file with all samples (280 samples) and the genotype file is (170).
I have a couple of questions:
1) I have multiple samples from different biopsy locations for each genotype ID (individual). Therefore the total number of individuals is less than the number of samples and I need all the samples for the purpose of this analysis. How does GEMMA handle this case? How should I make my phenotype file? Does GEMMA need the same number of genotypes and phenotypes?
2) The genotype file is in Plink format. I made the kinship matrix using plink. I have all bed/bim/fam files in my directory. Though my phenotype file is the expression dataset. if I define the phenotype data as the expression data file, does the program read .fam or the expression.txt data file?
the GEMMA code
~/gemma-0.98-linux-static -bfile tmp.analysis -p tmp.expression.txt -km 1 -k ../Kinship/IBS.mibs -lmm 4 -o $line.outcome -miss 0.99
I appreciate any help and direction in this regard, SN