I have RNAseq data from 10 different condition with two biological replicates each. I have run Kallisto on all the samples with 100 bootstraps.

I passed all the samples to Sleuth for analysis with a reference table as mentioned in the *"getting started"* page.

```
sample condition
A1 A
A2 A
B1 B
B2 B
C1 C
C2 C
```

...and so on.

I fitted the model as described in the *"getting started"* page and exported the results obtained by

```
results_table <- sleuth_results(so, 'reduced:full', test_type = 'lrt')
```

I export this table as a CSV file with columns which include p-value and q-value (and other metrics). What I do not understand is what do these p-values signify. What happens when multiple conditions are passed; does Sleuth do a pairwise comparison? If that is so then there should be a p-value/q-value (and other values) for each pair. I am not getting that.

When I input multiple conditions then do p-values denote differential expression in *all the conditions* or *at least one condition*?

If possible also let me know (some page/resource on) what other models can be fit on the data (from the *"getting started"* example, it appears that different models are possible but the manual and the preprint do not mention anything other than the intercept-only model).

This can be of any help: https://groups.google.com/forum/#!forum/kallisto-sleuth-users

I posted a question there but it was not answered!