Hi, I am doing an analysis to see if these is tissue specific effects on the gene expression data .
Our data were collected from 6 different labs (batch effects). lab 1 has tissue type 1 and tissue type 2, lab 2 has tissue 3, 4,5,6. The other labs has one tissue type each. The 'sample' data is as below: ------------------------------------------------------------------------------------------------ Sample.ID Gene tissue.type batch(lab) expression.level id1 gene1 liver batch1 0.67 id1 gene2 liver batch1 0.89 id2 gene1 kidney batch1 0.52 id2 gene2 kidney batch1 0.45 . . id10 gene1 brain batch4 0.56 id10 gene2 brain batch4 0.97 . . id100 gene1 skin batch10 0.98 id100 gene2 skin batch 10 0.87 ----------------------------------------------------------------------------------------------------- I am going to use 'aov' to compare the tissue-specific average of gene expression. 'tissue.type' is the fixed effects, 'batch' and 'Sample.ID' are the random effects (to control for inter-individual variation and batch effects). How should I write my 'aov' function? I am not sure about the 'random effects' part i.e. fm <- aov(expression.level~tissue.type+Error(Sample.ID)+Error(batch), data=sample) ?? Thank you, karena -- View this message in context: http://r.789695.n4.nabble.com/A-question-regarding-random-effects-in-aov-function-tp3827719p3827719.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
