[BioC] hoeffd function (CRAN HMisc package) use in arrayQualityMetrics

[jerry davison [guest]]

ArrayQualityMetrics uses hoeffd to assess any linear relationship between M and A in MA plots and flags arrays where D > 0.15.  Some of the matrices I'm evaluating have NA's; those result from filtering, for example in applying Illumina beadarray detection p-value rules.

As you can see from evaluating the script below, NA's affect hoeffd.  In my situation, arrays with no strong linear relationship are flagged by this AQM measure.

Is this a bug in hoeffd?  Should AQM address this, perhaps by removing NA's in M and A before applying hoeffd?

# Filename: hoeffd.R
#
# Test Hmisc hoeffd() response to NA's in a matrix.  Used by # AQM to assess outliers in the MA plots.
# 
# J Davison 5dec2013
#
#--> source('hoeffd.R',echo=TRUE,max=Inf)
#

library(Hmisc)
library(arrayQualityMetrics)

set.seed(11)
M = runif(10)*10

set.seed(7)
A = runif(10)*10

df1 = data.frame(M, A)
hoeffd(as.matrix(df1))$D
#        M      A
# M 1.0000 0.0437
# A 0.0437 1.0000

### Add NA's
df2 = rbind(df1, data.frame(M=rep(NA, 2), A=rep(NA, 2)))
hoeffd(as.matrix(df2))$D
#        M      A
# M 1.0000 0.0959
# A 0.0959 1.0000

### Add more NA's
df3 = rbind(df1, data.frame(M=rep(NA, 4), A=rep(NA, 4)))
hoeffd(as.matrix(df3))$D
#       M     A
# M 1.000 0.163
# A 0.163 1.000




 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] splines   grid      stats     graphics 
[5] grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] arrayQualityMetrics_3.18.0
[2] Hmisc_3.13-0              
[3] Formula_1.1-1             
[4] survival_2.37-4           
[5] lattice_0.20-24           
[6] cluster_1.14.4            
[7] BiocInstaller_1.12.0      

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.23.28 BeadDataPackR_1.14.0 
 [3] Biobase_2.21.7        BiocGenerics_0.7.8   
 [5] Biostrings_2.30.0     Cairo_1.5-2          
 [7] DBI_0.2-7             IRanges_1.20.5       
 [9] RColorBrewer_1.0-5    RSQLite_0.11.4       
[11] SVGAnnotation_0.93-1  XML_3.98-1.1         
[13] XVector_0.1.4         affy_1.39.6          
[15] affyPLM_1.38.0        affyio_1.29.5        
[17] annotate_1.39.0       beadarray_2.12.0     
[19] colorspace_1.2-4      gcrma_2.34.0         
[21] genefilter_1.43.0     hwriter_1.3          
[23] latticeExtra_0.6-26   limma_3.18.2         
[25] parallel_3.0.2        plyr_1.8             
[27] preprocessCore_1.23.0 reshape2_1.2.2       
[29] setRNG_2011.11-2      stats4_3.0.2         
[31] stringr_0.6.2         vsn_3.29.1           
[33] xtable_1.7-1          zlibbioc_1.7.0       


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