Question: model.matrix in metagenomeSeq
0
gravatar for PJ
4.1 years ago by
PJ0
United States
PJ0 wrote:

Hi,

I am running fitZig for differential abundance testing. When I place:

treatment=pData(obj)$Treatment

Before=pData(obj)$Time

normFactor=normFactors(obj)

normFactor=log2(normFactor/median(normFactor)+1)

mod = model.matrix (Treatment + Before + normFactor), the answer is:

Error: $ operator is invalid for atomic vectors

Based on internet there is  an error when applying $ to a vector. But how can I fix the problem in the script? 

Thanks!!

PJ

 

fitzig • 827 views
ADD COMMENTlink modified 4.1 years ago by Hector Corrada Bravo60 • written 4.1 years ago by PJ0
Answer: model.matrix in metagenomeSeq
0
gravatar for Hector Corrada Bravo
4.1 years ago by
United States
Hector Corrada Bravo60 wrote:

Missing '~' in the formula specification?

mod = model.matrix(~Treatment+Before+normFactor)
ADD COMMENTlink written 4.1 years ago by Hector Corrada Bravo60
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