Question: (1) Anova for 12 Affy yeast chips (Yg98) // (2) Problem fitting Li&Wong model with Affy 1.0 :

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julien.sylvestre@wotan.ens.fr •

**50**wrote:(1) Anova for 12 Affy yeast chips (Yg98)
I'm going to try to explain the problem in a better way. I have the
following experimental design :
Fraction 1
Fraction 2 Medium A
Fraction 3 * Medium B * 2 Reps
- Fractions 1, 2 and 3 are three distinct subcellular mRNA populations
;
- Medium A and B are two distinct culture medium ;
- By Rep is meant a 'biological repetition'. That is cells harvested
independantly from which the 3 Fractions are extracted. I have two
sets of three Fractions in Medium A and two sets of three Fractions
in
Medium B.
I am interested in finding - in a given medium - the distribution of
each mRNA among the 3 Fractions.
I thougth the data quite suited for ANOVA, at least as a first
analytic step.
The model would explain the log expression value by the sum of :
- a constant term (maybe null actually)
- a gene effect : approximately 6000 levels
- a fraction effect : 3 levels
- a medium effect : 2 levels
- a rep effect : 2 levels for each medium
- and possibly all two-order interactions.
As wrote before, I couldn't apply directly 'lm' or 'aov' in R due to
memory problems (the matrix to inverse being too large). Nor could I
use Matlab Stat toolbox 'anovan' function which resulted in a disaster
or
the 'MANOVA' free matlab toolbox which is clearly specialised in cDNA
array data. I am to try SAS 'proc anova' soon which should at least
provide me average effects (that I admit are not so interesting by
themselves). Before I calculate the whole thing myself, as a last
solution, I wanted to make sure nobody had the idea of a particular
tool to use directly or adapt easily. I looked rapidly at the 'Anova'
function
in the Genefilter package but it seems to use lm and to be limited to
a one-way analysis hence I didn't find how to take advantage of it.
(2) Problem fitting Li&Wong model with Affy 1.0 :
I get almost the same problem wusing the cel.container mechanism
(actually I didn't try it before because I thought I was to use a
command called read.cel.container which in fact does not seem to
exist) :
> myfiles = c("xxx1.cel", "xxx2.cel",...)
> lcel = read.container.celfile(filenames = myfiles
> cdf = read.cdffile("Yg_s98.CDF")
> eset = generateExprSet(lcel, cdf, method = "liwong", normalize = F)
> eset = generateExprSet(lcel, cdf, method = "liwong")
9335 ids to go process...
instancianting an exprSet...
Error in data.matrix[, !phi.outliers] %*% phi[!phi.outliers] :
non-conformable arguments
> traceback()
4: which(cdf@name == i, arr.ind = TRUE)
3: locate.name(ids[id], cdf, type = "pm")
2: .local(x, cdf, method, ...)
1: generateExprSet(lcel, cdf, method = "liwong")
Thank you.
JS.