[BioC] follow-up about 'express' in affy / ANOVA question:wq

[Laurent Gautier]

Oooops... the last part of the follow-up was in french (just realized it)..

As what is discussed could (still) be on general interest, I added a translation...


> 
> * Je n'ai pas essay? le 'Cel.container mecanism' ; ce qui me para?t ?trange c'est que cel? fonctionnait avant (version 0.8) et que ?a fonctionne avec d'autres m?thodes. 
<Translation: I did not try with Cel.container. It looks strange since it was working in version 0.8 and that it functions with other methods...>

It could be caused by the nature of your data (Rafael could correct me/ add details about that... could the late addition about 'background correction' be involved ?).

The Cel.container mecanism is described in the vignette ('affy.pdf'). To use it,
you will have to call the step you want to use manually. In your example
(note: you do not normalize. I assume you do that with good reasons):

filenames <- c("path/to/file1.CEL", "path/to/file2:CEL",  <and so on>)
lcel <- read.container.celfile(filenames=myfiles)
cdf <- read.cdffile("path/to/my/cdf.file.CDF")
eset <- generateExprSet(lcel, cdf, method="liwong")



> Pour information, j'obtiens ?a en tapant 'traceback()':
> 6: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, 
>        normal.resid.quantile, large.threshold, large.variation, 
>        outlier.fraction, delta, maxit, outer.maxit, verbose)
> 5: FUN(X[[3]], ...)
> 4: lapply(as.list(X), FUN, ...)
> 3: sapply(data.lst, summary.stat, ...)
> 2: t(sapply(data.lst, summary.stat, ...))
> 1: express(pl1, normalize = F, summary.stat = li.wong)
<Translation: result of the traceback()>

> 
> * Je vais regarder genefilter, en fait je pensais que c'?tait tr?s orient? puces cDNA . Effectivement, l'id?al serait davoir une ANOVA g?ne par g?ne. 
<Translation: I'll look at genefilter, I thought it was mainly meant for cDNA arrays. It would be nice to have one ANOVA per gene.>


genefilter is not exactly what you want, thought learning how it work
will help you to achieve your goal. The function 'filtertheniter' could
also prove informative. If you do not succeed, just ask, I can come up with an
'out-of-the-box' working solution (sorry, busy today).





Hopin' it helps,



Laurent



--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			D-2800 Lyngby,Denmark	
tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent