compare protein abundance between WT and mut case
I have two cancer type cohorts, each cohort provides the abundance of protein values between wt and mut case. And I need to compare each mt with each mutant(ex. compare cell line1-wt with mutant1,cell line1 with mutant2) All these data has been normalized. For this kind of comparison, should I just do a T-test? Or Mann-Whitney-Wilcoxon Test? Since a lot of values of wt are missing and it seems non-parametric?
ex Breast cancer
cell line1-wt cell line2-wt cell line3-wt mutant1 mutant2 mutant3
TP53 Missing Missing Missing 4 5 3
BRCA Missing 4 Missing 7 6 6
MALAT 1 5 Missing 4 Missing
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You don't have replicates?
No replicates. Only compare between one wt type and one mut type. Should I use 2 sample t-test?
No, you can't get a meaningful p-value.