Felix,

You seem to be providing the correct inputs to Cuffdiff and it appears to be 
producing valid output. More information about setting parameter values and 
interpreting Cuffdiff can be found in manual: 
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff

Good luck,
J.

On Jun 16, 2011, at 8:13 AM, Felix Mayr wrote:

> Hi there,
> 
> Looking at the output of the SplicingDiff files of CuffDiff, me and my 
> colleagues are preplexed about the output of the p_values and q_values. We've 
> tried different inputs of different samples to compare but never seem to 
> manage to get p_values smaller than 0.50 and we keep getting higher than 1 
> q_values (also smaller which we expect) which we think is strange too. 
> 
> The input files we use for the CuffDiff are the CuffCompare of a combined 
> CuffCompare of a dataset, or the CuffCompare of just the two samples we want 
> to analyse. For the samples input files we use the TopHat files respectively. 
> 
> Could you please help us get meaningful results for the SplicingDiff files or 
> help us understand the data? 
> 
> The top 5 rows of our typical SplicingDiff file: 
>        test_id     gene_id gene                    locus sample_1 sample_2
> 1583  TSS11905 XLOC_028193    - chr5:134910259-134914719       q1       q2
> 2385  TSS12870 XLOC_030892    -   chr7:29976178-30008608       q1       q2
> 8005   TSS6887 XLOC_016656    -  chr18:47803031-47807892       q1       q2
> 10214  TSS9761 XLOC_022527    -  chr20:43128822-43138649       q1       q2
> 2818  TSS13383 XLOC_032450    - chr8:100899717-100905900       q1       q2
>     status value_1 value_2    sqrt.JS. test_stat  p_value  q_value
> 1583      OK       0       0 0.000771867  0.797878 0.501645 164.5400
> 2385      OK       0       0 0.001548470  0.797809 0.505482  82.8991
> 8005      OK       0       0 0.003288510  0.797717 0.508184  55.5615
> 10214     OK       0       0 0.001414180  0.797620 0.510277  41.8427
> 2818      OK       0       0 0.007112780  0.797416 0.513678  33.6973
> 
> Thanks in advance for your most appreciated help,
> 
> Felix Mayr
> 
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