[BioC] Encrypting IDAT files using IDATreader

[Mark Cowley]

Dear all,
I have been developing 'lumidat' which provides equivalents to lumi::lumiR and limma::read.ilmn which accept idat files. There's no compiled code (java handles the decryption), so it's easy to install on linux or mac.
I've used it on hundreds of arrays, so please contact me if you're interested in testing it out.

cheers,
Mark

On 28/08/2012, at 9:20 AM, Kasper Daniel Hansen wrote:

> You / we / someone should consider wrapping this into a more easy to
> install package, together with crlmm::readIDAT (and in case there are
> other Illumina parsing functions around, they could be included as
> well).  What is the license for openssl?
> 
> Kasper
> 
> On Sat, Aug 25, 2012 at 3:12 PM, Mike Smith <grimbough at gmail.com> wrote:
>> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>>        [[alternative HTML version deleted]]
>>> 
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>> 
>> 
>> 
>> --
>> Mike Smith
>> PhD Student
>> Computational Biology Group
>> Cambridge University
>> 
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> 
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