I am getting this error when I run "anotaPerformQc" with default parameters. I have no any zero value in the matrix (log2 transformed normalized FPKM). Could some body please help me out.

Error in quantile.default(as.numeric(x), c(0.25, 0.75), na.rm = na.rm,

missing values and NaN's not allowed if 'na.rm' is FALSE

In addition: Warning messages:

1: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

2: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

3: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

4: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

5: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

6: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

7: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

8: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

9: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

10: In anova.lm(tmpLm) :

ANOVA F-tests on an essentially perfect fit are unreliable

You will need to give the results from

`traceback()`

right after you get the error, as well as`sessionInfo()`

.That said, R isn't complaining about zeros - it says there are either missing or NaN values. In addition, it also tells you that you cannot use na.rm = FALSE. Have you tried adding a na.rm = TRUE to your function call? I haven't looked at the code to see if there is an ellipsis argument to pass arbitrary arguments to helper functions, but if there is such an argument, that might help.