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One way ANOVA using cuffdiff?
Dear All
This might be a question somewhere in their manual or has been asked and answered many times in this forum.
In my analysis, I have 3 groups (each containing 3 biological replicates) and I want to compare among them in a one-way ANOVA setting.
I tried to run cuffdiff with all 9 samples entered exactly as the example illustrated. However, the cuffidff only provided me in the gene_exp.diff file with differentially expressed genes from comparisons of the first 2 conditions.
So I wonder if I did the procedure wrong or they simply do not have a one-way ANOVA setting in cuffdiff.
Also, is there a nonparametric option in cuffdiff?
Thanks a lot
This might be a question somewhere in their manual or has been asked and answered many times in this forum.
In my analysis, I have 3 groups (each containing 3 biological replicates) and I want to compare among them in a one-way ANOVA setting.
I tried to run cuffdiff with all 9 samples entered exactly as the example illustrated. However, the cuffidff only provided me in the gene_exp.diff file with differentially expressed genes from comparisons of the first 2 conditions.
So I wonder if I did the procedure wrong or they simply do not have a one-way ANOVA setting in cuffdiff.
Also, is there a nonparametric option in cuffdiff?
Thanks a lot