18 months ago by
Using your case as an example, with three species (A, B, C) and three experimental conditions per species (1, 2, 3), if you ran each experimental condition of species A as a 'condition' in Cuffdiff, you would return all possible comparisons between the three samples. Your differential expression testing file would have fold change values for A.1 vs A.2, A.1 vs A.3, and A.2 vs A.3.
If you are interested in comparing all nine samples against each other, you would assign each sample as one condition and Cuffdiff will perform all possible comparisons between your nine samples.
Just a note here, the 'FPKM tracking' files will have one transcript/gene per line with FPKM information for each condition tested represented as a series of columns. The 'differential expression testing' file will have one line for each transcript/gene for each comparison. For example, if you have 10,000 transcripts in your reference and do the three way comparison (as above), the 'transcript FPKM tracking' file will have 10,000 lines and the 'transcript differential expression testing' file will have 30,000 lines.
Hope this helps.
Thanks for using Galaxy!
Mo Heydarian, Galaxy Team