Question: What is the Sleuth intercept and how can Sleuth be used when you have >2 treatment types?
gravatar for james.lloyd
3.7 years ago by
United States
james.lloyd100 wrote:

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

dte rna-seq kallisto salmon sleuth • 1.8k views
ADD COMMENTlink modified 22 months ago by lalvarez10 • written 3.7 years ago by james.lloyd100

Do you have an update you could share?

ADD REPLYlink modified 26 days ago • written 26 days ago by sredemption0
gravatar for lalvarez
22 months ago by
lalvarez10 wrote:

Did you get it?

I'm now in the same situation.



ADD COMMENTlink written 22 months ago by lalvarez10
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