Cuffdiff time series with biological replicates

[dvanic]

Hi! Sorry if this is a silly question, but when doing a time series comparison in cufflinks how do I specify that I have three replicates for each time point?

Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)

I have
-T first, first, first, second, second, second, third, third, third

How do I make sure cuffdiff understands this and calculates the variance accordingly?

Thanks in advance!

[upper]

I have the sam question,how command write?

[Dario1984]

I also thought about this design when I read the documentation. The option description could be more explicit. My impression is that it can't handle replicates in a time series design.

[dvanic]

Uggh. Yet another reason not to use cufflinks... but nothing quite tries to do what it does...

[sBeier]

I am not sure from your example, so I am asking this. Intuitively I would have tried the same like with the normal input:
-T A1,A2,A3 B1,B2,B3 C1,C2,C3
Meaning, separating samples with spaces, replicates with comma (and without space after the comma).

[glados]

Wondering this as well.