What is the Sleuth intercept and how can Sleuth be used when you have >2 treatment types?
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7.7 years ago
james.lloyd ▴ 100

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

RNA-Seq sleuth kallisto salmon DTE • 3.4k views
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Did you get it?

I'm now in the same situation.

Thanks!!

LucĂ­a

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Do you have an update you could share?

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