Dear expert,

I am using crlmm and VanillaICE for copy number inference with human660quadv1. I have try follow code, but I get a error and warnings.

library("crlmm")
library("VanillaICE")
library(ff)
ocProbesets(150e3)
ocSamples(500)
samplesheet <- cbind(phenotype,paste(phenotype[,2],phenotype[,3],sep="_"))
colnames(samplesheet) <- c("samplename","SentrixBarcode_A","SentrixPosition_A","filename")
batch <- factor(rep("b",nrow(samplesheet)))
arrayInfo <- list(barcode=NULL, position="SentrixPosition")
arrayNames <- file.path(datdir,samplesheet[, "filename"])
gensnp <- genotype.Illumina(sampleSheet=samplesheet,
        arrayNames=arrayNames,
        copynumber = T,
        arrayInfoColNames=arrayInfo,
        cdfName="human660quadv1a",
        batch=batch,
        verbose=T)
library(oligoClasses)
library(VanillaICE)
library(crlmm)
library(SNPchip)
library(IRanges)
library(foreach)
registerDoSEQ()
se <- as(gensnp, "SnpArrayExperiment")
#library(ArrayTV)
#i <- seq_len(ncol(se))
#increms <- c(10,1000,100e3)
#wins <- c(100,10e3,1e6)
#res <- gcCorrect(lrr(se),
#        increms=increms,
#        maxwins=wins,
#        returnOnlyTV=FALSE,
#        verbose=TRUE,
#        build="hg18",
#        chr=chromosome(se),
#        starts=start(se))
#se2 <- se
#assays(se2)[["cn"]] <- res$correctedVals
res <- hmm2(se2)
filter_param <- FilterParam()
show(filter_param)
cnvFilter(res, filter_param)
select_cnv <- FilterParam(state=c("1", "2", "5", "6"), seqnames="chr22")
cnvs <- cnvFilter(res, select_cnv)
cnvs

The warning is from : se <- as(gensnp, "SnpArrayExperiment")

se <- as(gensnp, "SnpArrayExperiment")
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

There were 24 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In calculateRBafCNSet(object, batch.name, chrom) :
  Only computing log R ratios and BAFs for autosomes and chr X
2: In integerMatrix(lrr, 100) : NAs introduced by coercion
3: In integerMatrix(lrr, 100) : NAs introduced by coercion
4: In integerMatrix(lrr, 100) : NAs introduced by coercion

The error is:

> res <- hmm2(se)
Error in { :
  task 1 failed - "error in evaluating the argument 'x' in selecting a method for function 'NA_filter': Error in `[.ff`(list(), 1L, drop = FALSE) :
  unused argument (drop = FALSE)
"

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  datasets  utils     stats     graphics  grDevices
[8] methods   base     

other attached packages:
 [1] ArrayTV_1.4.0               Biobase_2.26.0             
 [3] foreach_1.4.2               SNPchip_2.12.0             
 [5] human660quadv1aCrlmm_1.0.3  ff_2.2-13                  
 [7] bit_1.1-12                  VanillaICE_1.28.3          
 [9] GenomicRanges_1.18.1        GenomeInfoDb_1.2.2         
[11] IRanges_2.0.0               S4Vectors_0.4.0            
[13] BiocGenerics_0.12.0         crlmm_1.24.0               
[15] preprocessCore_1.28.0       oligoClasses_1.28.0        
[17] nutshell_2.0                nutshell.audioscrobbler_1.0
[19] nutshell.bbdb_1.0           faraway_1.0.6              
[21] MASS_7.3-35                

loaded via a namespace (and not attached):
 [1] affyio_1.34.0        base64_1.1           BiocInstaller_1.16.1
 [4] Biostrings_2.34.0    chron_2.3-45         codetools_0.2-9     
 [7] compiler_3.1.1       data.table_1.9.4     DNAcopy_1.40.0      
[10] ellipse_0.3-8        grid_3.1.1           illuminaio_0.8.0    
[13] iterators_1.0.7      lattice_0.20-29      Matrix_1.1-4        
[16] matrixStats_0.10.3   mvtnorm_1.0-0        plyr_1.8.1          
[19] R.methodsS3_1.6.1    Rcpp_0.11.3          RcppEigen_0.3.2.2.0
[22] reshape2_1.4         splines_3.1.1        stringr_0.6.2       
[25] VGAM_0.9-5           XVector_0.6.0        zlibbioc_1.12.0