knnimp.internal error

[yeswzc]

Hi Yinan,
I am using REMP to impute TCGA LUAD 450 methylation data. I tried to impute DNA methylation data after filtered probes with missing raio > 20%. However, an error occured:
Error in knnimp.internal(x, k, imiss, irmiss, p, n, maxp = maxp) : NA/NaN/Inf in foreign function call (arg 1) Calls: grooMethy -> <Anonymous> -> knnimp -> knnimp.internal Execution halted
Do you know what is happens, and how to solve it?

Thanks!

[YinanZheng]

I could not replicate your error. Please see my code and verbose message. Hope it is helpful.

dat <- read.table(file = "./HumanMethylation450", header = TRUE, sep = "\t", row.names = 1)
missing_ind <- which(rowMeans(is.na(dat)) > 0.2)
dat_sub <- dat[-missing_ind,]

dat_groom <- grooMethy(dat_sub, verbose = TRUE)

Illumina 450k Methylation data in beta value detected.
A total of 16357 zero beta values are found.
Fixing 'zero' beta values with the smallest non-0 beta value = 1e-04 ...
A total of 9116 one beta values are found.
Fixing 'one' beta values with the largest non-1 beta value = 0.9999 ...
A total of 120318 NA/NaN/Inf values are found.
Converting beta/percentage value to M value ...
Imputing missing values using KNN method ...
All imputed probes are within the original data range.
Methylation data grooming is completed. (189 sec.)

[yeswzc]

Hi, I was using R version 3.5 which gave the error. I tested again using R version 3.5, this time it worked.
Thank you!