Hi to all,
i have preprocessed a large data set with 34 cel files and i want to compare some important factors implemented from the phenoData object. But one of my major concerns about using limma for more than one variable, is that one specific variable that i want to test regarding differential expression between metastatic and non-metastatic cancer samples, lacks appropriate sample comparison, as the metastatic cancer samples are only two and the non-metastatic cancer samples are 15. In other words, i believe that probably the statistical implementation is inappropriate because of the possible luck of statistical power, regarding the significantly fewer number of samples in the one condition. Also, is a multifactor experiment with two variables(including the one i mentioned called metastatic factor). Any suggestions or directions ?