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

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