Hi Sean,

You are right. I agree. Biologically, it may not be possible to compare
because of the experimental conditions. But can it be done just
statistically.

-Yogesh



On 15 September 2010 12:49, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> 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
>

	[[alternative HTML version deleted]]

