On Thu, Sep 6, 2012 at 6:46 AM, suparna mitra < mitra@informatik.uni-tuebingen.de> wrote: > Hello Group, > I am new in Bioconductor. I want to use it for my microarray data analysis. > Previously i was using different softwares for this. And this is my first > try with Bioconductor for big experiment. So thought to get some advice in > the beginning. > I have Three groups of patient: (In-vivo) > A-Acute reaction. Patient taking a drug X develops reaction. > R-recovered (6 weeks after acute reaction-not longer taking X). > T-Tolerant. Patient on X and tolerating treatment. > > Now in in-vitro study we used another constant Y > RXY recovered and challenged with X+Y > RY recovered challenged with only Y. RXY vs RY are to exclude effects by > Y. > TXY tolerant and challenged with X+Y, > TY tolerant challenged with only Y. TXY vs TY are to exclude effects by > Y. > > No I want to check the cross relation and effects A vs R, RvsT and Avs T > and differentially expressed genes for each comparison. There are not same > patients in different groups, thus I think I want to apply unpaired-t test. > > Any help will be really great. > Hi, Mitra. It sounds like you should take a look at the limma package. The limma user guide is extensive, but it is worth reading end-to-end. Give that a try and see how far you get. Sean [[alternative HTML version deleted]]