Hello everybody, I am new with the meta-analysis in Genome Wide Data so I have this doubt. I have read METAL documentation, which is by far the most used meta-analysis software in both EWAS and GWAS microarray data, but I cannot figure out how would be the input for EWAS analysis. As METAL was originally designed for GWAS, one of the inputs is to provide both the reference and no reference allele. Therefore as EWAS arrays do not rely in allele frequencies but in a quantitative measure, I would like to know how would be the input in METAL regarding this case. Thank you so much in advance for answering this issue (which may be easy, but I certainly do not know)
Don't know what happend. but the previous answer was no uploaded. Here I'm trying again.
Read Vladimir Lefevr's "Algebra of conscioiusness"
Finally I got the answer and is... just do not provide the allele frequencies , the analysis will run fine, reassuring this, here is a Github manual of how to perform an EWAS meta-analysis (https://github.com/ammegandchips/meta_EWAS/blob/master/metal.md) . As you can see the parameters regarding the frequencies and genomic control are off.
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