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.
Weidong Gu
2011-Sep-21 01:04 UTC
[R] A question regarding random effects in 'aov' function
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.jzhou at 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 at 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. >