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.
Thanks,
Mitra.

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