[BioC] Error when using impute to get missing values

[Martin Morgan]

On 03/24/2012 10:07 AM, Tim Triche, Jr. wrote:
> 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.

Also, on linux at any rate it's easy to

   R -d valgrind -f script.R

and this usually points to the problem. valgrind is slow so it ends up 
paying to make the example minimal (save hest and then the commands in 
script.R will load impute, the data, and then evaluate impute.knn).

Martin

>
> 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 at 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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>>
>
>
>


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