[BioC] Encrypting IDAT files using IDATreader

[Henrik Bengtsson]

I started a draft of an illuminaIO package for the purpose of setting
up one single Illumina file parser package (cf. affxparser):

  https://r-forge.r-project.org/scm/viewvc.php/pkg/illuminaIO/?root=aroma-dots

My strategy was to add to it as I needed new features myself, add
system tests, and when it would be of value to others I would put it
on CRAN.  From its NEWS:

Version: 0.2.1 [2012-02-07]
o CLEANUP: readIDAT() and readBPM() no longer give warnings about
  using readBin(..., signed=FALSE).

Version: 0.2.0 [2012-02-07]
o Added a NAMESPACE.

Version: 0.1.0 [2011-03-28]
o Copied readIDAT() and readBPM() from the crlmm package, which uses
  the Artistic-2.0 license.  However, the two functions originate
  from Keith Baggerly, MD Anderson.
o Created.

So, it's pretty much what is in crlmm (as of March 2011) with some
minor improvements.

Feel free to take it over, incorporate whatever, or simply ignore it.

/Henrik

On Mon, Aug 27, 2012 at 6:00 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> BSD (actually a dual BSD license from SSLeay)
>
> http://www.openssl.org/source/license.html
>
>
>
> On Mon, Aug 27, 2012 at 4:20 PM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> 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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>
>
>
> --
> *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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