[R-sig-ME] ANOVA for large data sets

[Aneta]

 Hi Everyone,
I am very new to R programming and I need your help regarding two way ANOVA model.
I have one variable (response) and three factors (Source, Batch and Time). I am always going to have a difference within time so probably I do not want to include it (??) in the analysis. 
I need to identify if there is a difference between the Source. I know how to run the test for one sample. However I do not know how to process multiple samples (large data sets) with multiple variables sharing the same three factors.
Please help me out! Please let me know if you need more clarification and I will be happy to provide it to you.
I am looking forward to your response.
Best!
Aneta
	[[alternative HTML version deleted]]