[BioC] import data for limma analysis

[Gordon Smyth]

At 08:23 PM 3/03/2004, Tineke Casneuf wrote:
>The problem is that I have a very large
>dataset, with more than 50 experiments (so 300 datasets, since replicates
>were used). I have written some scripts, so that calculating the averages and
>
>ratios is easy and fast. If it would be better for my research however to
>analyse the data with bioconductor (thereby I mean the functions
>model.matrix, makeContrasts, contrasts.fit), I still can do that (it would
>just take more time). I don't really understand what the 'advantage' is of
>using the linear fit. I know what a linear fit is, but I understand how it is
>
>done on microarray data, or what happens to the data.
>
>If it's not needed I guess I can do this (please correct me if I'm wrong):
>- import the data (genes horizontal and experiments vertical), with the names
>
>of the genes as row names and the log ratios in the table:
> > scan("list_of_genes", what = "list") -> genes
> > read.table(file = "signals_in_table", row.names = genes) -> data
>
>[- Instead of using the expressions in the limma tutorial:
> > data <- ReadAffy()
> > eset <- rma(data)]
>
>[- So since I have already calculated the averages of the replicates and the
>ratios between experiments and controls, I guess I can also skip these
>commands:
> > design <- model.matrix(~ -1+factor(c(1,1,1,2,2,3,3,3)))
> > colnames(design) <- c("group1", "group2", "group3")
> > contrast.matrix <- makeContrasts(group2-group1, group3-group3,
>group3-group1, levels=design)]
> > fit <- lmFit(data, design)
> > fit2 <- contrasts.fit(fit, contrast.matrix)]
>
>- To find the differential expressed genes, can I just perform this function
>on my data?
> > fit2 <- eBayes(data)

Err ... No.

As I said in my reply to you on this list a few days ago, given your 
summarized data you can't do any statistical analysis. Just stick with the 
averages and log-ratios you've computed yourself.

Gordon

>Tineke
>
>--
>==================================================================
>Tineke Casneuf          Tel: 32 (0)9 3313692
>DEPARTMENT OF PLANT SYSTEMS BIOLOGY           Fax:32 (0)9 3313809
>GHENT UNIVERSITY/VIB,    Technology Park 927, B-9052 Gent, Belgium
>Vlaams Interuniversitair Instituut voor Biotechnologie         VIB
>e-mail:ticas at psb.ugent.be     http://www.psb.ugent.be/bioinformatics/