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Filippis, Ioannis
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30
@filippis-ioannis-4720
Last seen 9.7 years ago
Hi,
I am trying to run fitNbinomGLMs but depending on the factor selected,
it gives error "Error: NA/NaN/Inf in foreign function call (arg 1)".
The counts matrix doesn't have any Na/NaN values, I cannot really
understand what the problem is. I guess it shouldn't work for any
factor if there was any problem with gene counts.
> pData(cdsFull)
sizeFactor condition type
wtH1 2.17904027 treated a
wtP1 0.24260614 treated b
prH1 1.42343596 untreated a
prP1 0.14120460 untreated b
wtH4 3.45554434 treated a
wtP4 2.38048956 treated b
prH4 4.13642641 untreated a
prP4 0.40209227 untreated b
wtH7 3.76575182 treated a
wtP7 0.88389937 treated b
prH7 2.98917685 untreated a
prP7 0.08601356 untreated b
> head(counts(cdsFull))
wtH1 wtP1 prH1 prP1 wtH4 wtP4 prH4 prP4 wtH7 wtP7 prH7 prP7
1 12 3 5 0 12 30 10 0 8 11 11 0
2 195 14 99 0 14 31 38 2 36 12 39 1
3 135 25 112 15 482 252 321 34 233 73 175 4
4 149 11 119 22 525 181 828 92 998 181 1086 19
5 6 0 8 0 5 3 3 0 2 0 12 0
6 39 2 4 21 77 120 26 192 35 15 6 11
> fit0<-fitNbinomGLMs(cdsFull, count ~ type)
.............
There were 26 warnings (use warnings() to see them)
> fit1<-fitNbinomGLMs(cdsFull, count ~ condition)
..........Error: NA/NaN/Inf in foreign function call (arg 1)
In addition: There were 21 warnings (use warnings() to see them)
> fit1<-fitNbinomGLMs(cdsFull, count ~ condition + type)
Error: NA/NaN/Inf in foreign function call (arg 1)
In addition: Warning message:
glm.fit: algorithm did not converge
Many thanks for your help.
Best,
Ioannis
