[BioC] import data for limma analysis

[Gordon Smyth]

At 11:20 PM 1/03/2004, Tineke Casneuf wrote:
>This question may have been asked, but I can't find the asnwer on the
>mail archive. I am trying to find a way to identify differentially
>expressed genes; I was recommended to use limma. I read in the manual
>that I can use data analysed with other packages (like affy and others)
>or that I can import data from a software program, like ArrayVision,
>ImageGene, GenePix and others.
>
>But I have Affymetrix data that are already normalised (with Affy
>software);

Just import your data into R using read.table() etc. All you need is a 
matrix of log-expression values.

>I have also calculated averages (for the replicates) and
>ratios (between experiments and controls).

No one can help you very much if you've already summarized your data in 
this way. You've effectively already done your own analysis. If you want 
help from limma or other analysis packages, you need to go back to the 
original normalized data as it came out of the MAS program.

Gordon

>  All my data are in csv-files.
>I was wondering whether I can import it from my own csv files and how to
>do this (read.table() for the data and scan() for the gene names) . Or
>should I import the data from the experiments and controls separatly and
>then go on using the commands in the tutorial (model.matrix, c, lmFit,
>makeContrasts, contrasts.fit, eBayes) or do I need to do more with my
>data or maybe omit steps?
>
>Thank you very much in advance!
>
>--
>==================================================================
>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/