[BioC] paired t test question ?

[Gordon Smyth]

Dear Philippe,

I would personally use the affy package to do the normalization, then use 
functions exprs and se.exprs to extract the expression levels and se's as 
matrices, then would use the functions lm.series and ebayes from the 
SMAWEHI package (not yet on bioconductor but soon to be) to construct all 
the tests and comparisons simultaneously.

I apologize for directing you off-site from bioconductor.org, but SMAWEHI 
is currently available only from http://bioinf.wehi.edu.au/smawehi

Regards
Gordon

At 03:39 PM 14/03/2003, Phguardiol at aol.com wrote:
>I m using Affy U133a/b and experiments have been run in duplicates, but 
>also with 2 different conditions (with and without drug) so for each cell 
>line I can use 4 chips to search for genes always differentially expressed 
>between the corrected and the uncorrected.
>Hoping that I am clear enough !
>Thanks for your input
>Philippe

---------------------------------------------------------------------------------------
Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3050, Australia
Tel: (03) 9345 2326, Fax (03) 9347 0852,
Email: smyth at wehi.edu.au, www: http://www.statsci.org