how to set one sample as a control for my other sample in gene differential analysis

[meghavarshney]

Hello everyone
I have a question.I have 3 stages of 2 diff genotype from a single tissue type i would like to chk differential gene expression analysis among these genotype at different stage. but to chk the gene that are specifically expressed in this particular tissue we also collect sample from one another tissue that may be vegetative or some other (it can be a used as a control for different stages ). so that we get to know what are the specific gene for this tissue. I would like to know how to compare or set other tissue as a reference for my tissue type.
how to set one sample as a control against other sample in gene differential analysis
can you suggest something on it ?

[AndrewO]

While you can compare the raw expression between the two phenotypes at the transcript/gene level, you will not be able to assess any kind of statically significant meaning (i.e. no p-value). It is generally recommended to have at least 3 samples of each phenotype you are trying to compare in order to generate/calculate a distribution and assess the likelihood of obtaining the measurement by random chance alone.