Cuffdiff splicing.diff

[Greg]

Hello everyone,

I just want to clarify the differences between two of the cuffdiff output files, splicing.diff and isoform_exp.diff. Splicing.diff tests whether or not the relative contribution of different isoforms is significantly different between treatments independent of the expression level of that gene (eg tissue 1 is 80/20 for two isoforms and tissue 2 is 50/50). Isoform_exp.diff tests if the expression level of the isoforms is different, this might say there is a significant difference in isoform levels even if the ratio of the different isoforms is the same across treatments. Do I have this correct/clear enough?

Also, in both cases I am getting the majority of isoforms are coming out as a NOTEST. Could I be doing something wrong or do I just not have enough depth?

thanks in advance!

[sindrle]

Hello everyone,

I just want to clarify the differences between two of the cuffdiff output files, splicing.diff and isoform_exp.diff. Splicing.diff tests whether or not the relative contribution of different isoforms is significantly different between treatments independent of the expression level of that gene (eg tissue 1 is 80/20 for two isoforms and tissue 2 is 50/50). Isoform_exp.diff tests if the expression level of the isoforms is different, this might say there is a significant difference in isoform levels even if the ratio of the different isoforms is the same across treatments. Do I have this correct/clear enough?

Also, in both cases I am getting the majority of isoforms are coming out as a NOTEST. Could I be doing something wrong or do I just not have enough depth?

thanks in advance!

If the ratio is constant.. How can you say individual isoforms changes..?