I am working with crlmm package for the chip
BDCHP-1X10-HUMANHAP550_11218540_C. The following is my code:
library(Biobase) library(crlmm) library(VanillaICE) library(lattice) library(ff) library(illuminaio) library("human550v3bCrlmm") library("human610quadv1bCrlmm") cnSet <- genotype.Illumina(sampleSheet=samplesheet, arrayNames=arrayNames, arrayInfoColNames=arrayInfo, cdfName="human550v3b", batch=batch) Instantiate CNSet container. path arg not set. Assuming files are in local directory, or that complete path is provided Initializing container for genotyping and copy number estimation Processing sample stratum 1 of 4 'path' arg not set. Assuming files are in local directory, or that complete path is provided in 'arrayNames' Loading chip annotation information. Quantile normalizing 100 arrays by 10 strips. |======================================================================| 100% Loading snp annotation and mixture model parameters. Calibrating 100 arrays. | | 0%Error in quantile.default(M, c(1, 5)/6, names = FALSE) : missing values and NaN's not allowed if 'na.rm' is FALSE
I tried to search where the
genotype.Illumina function is using
quantile.default so I can change the code, but I cannot find it. Has anyone faced this problem?