We are planning to perform an eQTL analysis where the genotype input, at this time, will only be from a previous genotyping microarray run.
In this case, would it still be appropriate for us to run the analysis using a traditional QTL algorithm (R/qtl method em) and using Cufflinks FPKM as phenotype input? I see many papers talking about doing analysis this way using microarray data, but not so much using RNA-seq data, and are not completely sure if the results are directly comparable...
Thanks for the help!
In this case, would it still be appropriate for us to run the analysis using a traditional QTL algorithm (R/qtl method em) and using Cufflinks FPKM as phenotype input? I see many papers talking about doing analysis this way using microarray data, but not so much using RNA-seq data, and are not completely sure if the results are directly comparable...
Thanks for the help!
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