I have 2 different cell lines (B cells and fibroblasts) with the same genbe deficiency and the corresponding corrected cell lines. What package (+ syntax) can I use in Bioconductor to run a comparison at the same time of the corrected versus deficient fibroblast and of the corrected versus deficient B cells ?
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.
Note added later: SMAWEHI was subsequently submitted to Bioconductor as the limma package.
At 03:39 PM 14/03/2003, Phguardiol@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