This is a recurring problem with impute.  I've tried tracing it and
eventually hit a dead end; if the bug is reproducible (it isn't always, for
me), running R as a gdb subprocess might help debugging it.  If you want, I
can give it a shot, time permitting; assuming this happens with this
experiment every time, send me a script to reproduce it (as in, retrieve
the data, put it in a matrix, and try imputing it) and I will see what I
can do.

Or ask the maintainer, Balasubramanian Narasimhan (help(package='impute')
for email address), who may be able to do it faster.  Or he may be busier.
 Could go either way :-)


On Sat, Mar 24, 2012 at 9:36 AM, David Westergaard
<s093629@student.dtu.dk>wrote:

> Hello,
>
> 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
>  /lib/libgcc_s.so.1
>
> 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)
>
> locale:
> [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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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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