[BioC] Encrypting IDAT files using IDATreader

[Mike Smith]

Hi Seungyeul,

IDATreader's a pretty experimental package, but it's worked on the few
systems I've tested it on.  The reliance on third party libraries is
why I've not submitted it to Bioconductor, so they may be causing
problems.

I'm not sure why you're using source(), rather than loading the
package via library().  Have you installed the package, or just
unzipped it and grabbed the .R file?  It need to be installed in order
to build the DLL and link against the decryption routines.  To do that
you need to download the tar.gz from the website you linked to and
then run

R CMD INSTALL IDATreader_0.1.1.tar.gz

in a terminal to installed the package.  You then need to load it using

library(IDATreader)

in your R session, rather than using source().

Hopefully that's of some help,

Mike



On 22 August 2012 23:35, Yoo, Seungyeul <seungyeul.yoo at mssm.edu> wrote:
> Hi all,
>
> I'm trying to analyze Illumina array of gene expression. The file format is .idat which is encrypted data.
>
> I downloaded IDATreader packages as Mike suggested in some of previous post. I also install openssl for my mac os x. http://www.compbio.group.cam.ac.uk/software/idatreader
>
> But when I tried to read idat file error message is prompted.
>
> source("/Library/R/readIDAT.R")
> filenames<-dir(patter="idat")
> idat<-readIDAT(file=filenames[1])
>
>> idat<-readIDAT(file=filenames[1])
> Decrypting to XML
> Error in .C("decryptSSL", as.character(file), as.character(tempFile),  :
>   C symbol name "decryptSSL" not in DLL for package "IDATreader"
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: i386-apple-darwin9.8.0/i386 (32-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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.4.7
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>
> Please let me have any advices to solve this problem.
>
> Seungyeul Yoo
>
> Postdoctoral Fellow
> Jun Zhu's Laboratory
> Institute of Genomics and Multiscale Biology
> Department of Genetics and Genomic Sciences
> Mount Sinai School of Medicine
>
>
>
>
>
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>
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-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University