I'd like to apply a t-student test to compare diferent samples to reference one using R but first I'm checking if my data meets the requirements for t-test so I removed outliers using the function rm.outlier() from Rcmdr R package and performed a Shapiro-Wilk test to check if replicates and the reference data are normaly distributed and now I should perform a test to check homogeneity of variance comparing each sample with the reference.
The samples has 3 replicates each one while reference has 11 replicates and samples and reference are independent.
I though about a Fisher Test but R says I need the same amount of replicates in the sample and reference. Then I though about Levene's Test and I tryed to run it in R using the built-int function in Rcmdr package according to this post http://stats.stackexchange.com/questions/262026/most-suitable-test-to-check-homogeneity-of-variances
On the other side, I'm performing a Wilcoxon test which does not need so many assuptions and at the end compare the "possitives" from t-student and wilcoxon. Or if one sample or reference does not meet one of the t.test ssumtions use de results provided by wilcoxon test.
What would be your suggestion?