On Wed, Sep 15, 2010 at 12:36 PM, Yogesh <yogeshp08@gmail.com> wrote: > Hi Sean, > > I have two GEO sets to compare (from two different experiments). I tried to > use limma package. But most of the packages use groups within a single > dataset for the t-test. I have 2 datasets with 24 time-points each. The > basic experiment in both cases is the same. I want to compare, say > time-point 0min vs. time-point 0min from both sets. I do not know what the > expression is. I want to check if the expression changes at a particular > time-point (from 0-24 time-points). I believe a line-chart or a volcano-plot > (single time-point or whole set) will help understand this better. > > You will not likely be able to compare the two datasets to each other using a t-test or any other test, for that matter, given the perfect confounding of experimental effect and lab/technical variation between the two datasets. Perhaps I am misunderstanding what you are trying to do, though. Sean > I thought I will ask for some guidance on how to go about it so that I can > try something in that direction. > > Thanks, > > -Yogesh > > > > On 15 September 2010 12:03, Sean Davis <sdavis2@mail.nih.gov> wrote: > >> >> On Wed, Sep 15, 2010 at 10:48 AM, Yogesh <yogeshp08@gmail.com> wrote: >> >>> Hello, >>> >>> I want to compare two GEO datasets based on the time series data. I want >>> to >>> be able to draw some visual highlighting/showing the difference in the >>> expression of the two sets. >>> >>> Can some one please guide me on how to go about it? >>> >>> >> Hi, Yogesh. >> >> It is not really possible to answer this question as your problem is much >> too vague. You will need to be much more detailed about what you are >> planning and what you have already done. >> >> Sean >> >> > > [[alternative HTML version deleted]]