Closed jmchan88 closed 3 years ago
Oh, actually as an update, I just realized I didn't see this warning message after running
zlmCond <- zlm(~mutation + time + cngeneson + treatment + mutation:time + time:treatment, sca)
Warning message: In .nextMethod(object = object, value = value) : Coefficients mutation:time are never estimible and will be dropped.
This is clearly the reason, but I wonder what is producing this warning exactly?
Probably one of your variables (either time or treatment) is aliased with mutation. What does
ftable(xtabs(~mutation + time + treatment, colData(sca))) say?
On Sep 17, 2020, at 4:47 PM, jmchan88 notifications@github.com wrote:
Oh, actually as an update, I just realized I didn't see this warning message after running
zlmCond <- zlm(~mutation + time + cngeneson + treatment + mutation:time + time:treatment, sca) Warning message: In .nextMethod(object = object, value = value) : Coefficients mutation:time are never estimible and will be dropped.
This is clearly the reason, but I wonder what is producing this warning exactly?
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As in one of the variables is collinear with mutation? In my data, only timepoint 0 is wild-type, so I guess that must be the issue? This is what that command shows:
In a nutshell, yes, you can't study an interaction between time and mutation, because there is no variation of time within the wild-type samples. The interaction measures if the time slope is different in the WT than in the mutant. But you can't fit a slope with a single data point as you have in the WT.
A second question that arises is if you want time as continuous or as a factor? However, having time as a factor still doesn't permit resolving an interaction between it and mutation.
On Sep 17, 2020, at 4:58 PM, jmchan88 notifications@github.com wrote:
As in one of the variables is collinear with mutation? In my data, only timepoint 0 is wild-type, so I guess that must be the issue? This is what that command shows:
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Ah gotcha makes perfect sense! Thank you so much! For the prompt help! Will close now!
Dear MAST team,
I'm trying to perform DEG particularly for an interaction term, but I get an error saying the interaction term is not found. For example, my code does the following:
However, I get the following error when running
Combining coefficients and standard errors Calculating log-fold changes Calculating likelihood ratio tests Error in generateHypothesis(hypothesis, colnames(object@coefD)) : Term(s) 'mutation:time ,' not found. Terms available: (Intercept) , mutation , time , cngeneson , treatment , time:treatment ,
Any help would be greatly appreciated! Thank you so much!
Joe