I mean if each system have specific number of samples and I want to know if there is a significant difference between all systems, if there are replicates and no replicates.
You need to give more detail about your study (e.g., what kind of variables you are measuring, what hypothesis you want to test) if you want to get a helpful answer.
I guess that you are talking of comparison of three groups with unequal sample sizes. If so, I can recommend one-way analysis of variance (ANOVA). If the samples are unequal in size, it is said to be unbalanced. If the ANOVA test is significant then there is significant difference between the systems.
Dear Ette this is exactly the case, where I have three cropping systems but each one have different number of samples bacause of many reasons such as area, I want to study the difference of soil C among those systems. As well, study the effect of depth and texture on soil C. What about dancn letters in this statistical analysis?