If different labs tested different tissue.types, I am not sure you can effectively partition variance between labs(batches) and tissue.types.
Weidong Gu On Tue, Sep 20, 2011 at 2:14 PM, karena <dr.jz...@gmail.com> wrote: > 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. > ______________________________________________ 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.
