Cuffdiff splicing.diff

Greg · 06-24-2010, 11:33 AM

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 · 11-04-2013, 05:04 PM

Quote:

Originally Posted by 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!

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

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06-24-2010, 11:33 AM	#1
Greg Member Location: British Columbia Join Date: Oct 2009 Posts: 31	Cuffdiff splicing.diff 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!