Error: missing values and NaN's not allowed if 'na.rm' is FALSE
0
2
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10 weeks ago
sunnykevin97 ▴ 970
setwd("/home/sun/Documents/genesite/pvalues/")

library(qvalue)

 p <- scan("/home/sun/Documents/genesite/pvalues  
/pvalues.txt",na.strings=T)

hist(p, breaks = 20, main = paste("Distribution of p-values"), xlab="Value")

aa <- is.na(p)

aa

[1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[20] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[39] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[58] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE


qobj <- qvalue(p, pi0.meth="bootstrap", fdr.level=0.05,na.rm=TRUE)

Error in quantile.default(pi0, prob = 0.1) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE

write.qvalue(qobj, file="qvalues.list")
Genome Software • 466 views
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3
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You should share the values with dput instead of just the results of is.na so we can check they are valid finite numeric values.

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0
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cat pvalues.txt
5.88E-05
1.42E-04
2.10E-04
2.24E-04
2.95E-04
3.07E-04
4.54E-04
4.66E-04
1.05E-03
1.80E-03
1.95E-03
2.02E-03
2.46E-03
2.76E-03
3.22E-03
3.66E-03
3.92E-03
4.14E-03
4.91E-03
5.79E-03
6.65E-03
7.09E-03
7.48E-03
7.93E-03
8.70E-03
9.76E-03
1.00E-02
1.03E-02
1.06E-02
1.13E-02
1.18E-02
1.26E-02
1.32E-02
1.44E-02
1.45E-02
1.54E-02
1.56E-02
1.61E-02
1.61E-02
1.72E-02
1.72E-02
1.77E-02
1.77E-02
1.87E-02
2.08E-02
2.27E-02
2.42E-02
2.43E-02
2.47E-02
2.54E-02
2.89E-02
2.89E-02
2.96E-02
3.06E-02
3.35E-02
3.44E-02
3.72E-02
3.88E-02
4.06E-02
4.15E-02
4.50E-02
4.51E-02
4.70E-02
4.84E-02
4.92E-02
5.02E-02
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Any suggestions ?

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co <- p.adjust(p, method = c("BH"),n = length(p))

[1] 2.160000e-05 2.160000e-05 4.725000e-05 2.314286e-05 9.000000e-06 9.000000e-06 2.314286e-05 2.160000e-05 5.800000e-05
[10] 4.355471e-02 4.355471e-02 3.442371e-02 4.355471e-02 3.442371e-02 2.333291e-02 4.960600e-02 3.132000e-02 2.333291e-02
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