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

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