What is the Sleuth intercept and how can Sleuth be used when you have >2 treatment types?

Question

[james.lloyd]

Hello Internet,

So I have an issue where I have more than one treatment. Treatment A, Treatment B, Treatment C and Treatment D (for example). I want to use kallisto or salmon to quant the transcripts and then use Sleuth to find differential transcripts. But I do not understand the commands very well.

When you run sleuth, you might get

models(so): coefficients: (Intercept) condTreatmentB condTreatmentC condTreatmentD

But what is (Intercept) and where is condition A? When I want to do differential testing between Treatment A and Treatment B, how do I do it? And then how do I change it to Treatment A and Treatment C? Or change it to Treatment B and Treatment C?

Please help me, you are my only hope.

Best, James

[lalvarez]

Did you get it?

I'm now in the same situation.

Thanks!!

Lucía

[sredemption]

Do you have an update you could share?

Answer 1

[bkleiboeker]

https://github.com/pachterlab/sleuth/issues/156