I have 3 groups of samples (A, B and C), and n=4 for each group (12 in total)
Question 1.
Cuffdiff output only gives group-level averaged fpkm. If i want to run some correlation tests for the gene expressions vs. phenotypic traits, how can i get the individual level of fpkm?
Question 2.
If i run cuffdiff in two ways:
- 3 groups altogether (GrpA,B,C) and let the program deal with the statistics (either ANOVA or T-test)
- 3 pair-wise comparisons (GrpA-B, GrpA-C, GrpB-C) one-by-one
I wonder at the end if i could get the same number of significantly expressed genes for each comparison, for example GrpA-B? Did any one test that before?
Thanks in advance!
Question 1.
Cuffdiff output only gives group-level averaged fpkm. If i want to run some correlation tests for the gene expressions vs. phenotypic traits, how can i get the individual level of fpkm?
Question 2.
If i run cuffdiff in two ways:
- 3 groups altogether (GrpA,B,C) and let the program deal with the statistics (either ANOVA or T-test)
- 3 pair-wise comparisons (GrpA-B, GrpA-C, GrpB-C) one-by-one
I wonder at the end if i could get the same number of significantly expressed genes for each comparison, for example GrpA-B? Did any one test that before?
Thanks in advance!
Comment