[BioC] Error when using impute to get missing values

David Westergaard s093629 at student.dtu.dk
Sat Mar 24 17:36:28 CET 2012


I am currently working on the dataset from ArrayExpress,
http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-1560. It has a
lot of missing values filled by null, and I am trying to fill these in
using impute.knn. However, when I try to do so, I get a lot of errors:
*** caught segfault ***
address 0x3f94a7e775b5bc59, cause 'memory not mapped'
aswell as
2000000007d68000-2000000007d78000 r-xp 00000000 08:03 235217090

which causes R to crash.

Sample code looks like:

# Read table, which contains two rows of headers
Data <- read.table(file=file,header=FALSE,stringsAsFactors=FALSE,sep="\t",skip=2,na.string='null')
hl <- readLines(file,2)
hl <- strsplit(hl, '\t')
names(Data) <- sub('_$', '', paste(hl[[1]], hl[[2]], sep="_"))
# Select only those columns which have the actual preprocessed value,
x <- c(1,grep("C57_T40_.*AGILENT_VALUE",names(Data),perl=TRUE))
signals <- Data[,x]
hest <- as.matrix(signals[,-1])
# Error occurs at this step.
hest2 <- impute.knn(hest)

Any help as to why this happens is greatly appreciated.

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: ia64-unknown-linux-gnu (64-bit)

[1] C

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

other attached packages:
[1] impute_1.28.0

Best Regards,
David Westergaard

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