Dear Mark,

Thanks for sharing "lumidat" package with me. I think it works fine now. But I'm wondering if an argument "convertNuID" is available in lumiR.idat(). When I ran it it failed with error like following.

> res<-lumiR.idat(filenames,manifestfile="HumanHT-12_V4_0_R1_15002873_B.txt",na.rm=TRUE,probeID="NuID",convertNuID=TRUE)
java -Xmx1024m -jar /Library/Frameworks/R.framework/Versions/2.15/Resources/library/lumidat/bin/IlluminaGeneExpressionIdatReader-1.0.jar -outputDir /var/folders/q6/hny37vrd5wx_77gpj71ng3cw0000gn/T//RtmpHnCFD6 -bg false -collapse none -manifestfile HumanHT-12_V4_0_R1_15002873_B.txt   '8473515005_A_Grn.idat' '8473515005_B_Grn.idat' '8473515005_C_Grn.idat' '8473515005_D_Grn.idat' '8473515005_E_Grn.idat' '8473515005_F_Grn.idat' '8473515005_G_Grn.idat' '8473515005_H_Grn.idat' '8473515005_I_Grn.idat' '8473515005_J_Grn.idat' '8473515005_K_Grn.idat' '8473515005_L_Grn.idat'
iDAT files: [8473515005_A_Grn.idat, 8473515005_B_Grn.idat, 8473515005_C_Grn.idat, 8473515005_D_Grn.idat, 8473515005_E_Grn.idat, 8473515005_F_Grn.idat, 8473515005_G_Grn.idat, 8473515005_H_Grn.idat, 8473515005_I_Grn.idat, 8473515005_J_Grn.idat, 8473515005_K_Grn.idat, 8473515005_L_Grn.idat]
Wrote: Sample Probe Profile.txt
Wrote: Control Probe Profile.txt
Error in lumiR(files[1], detectionTh = detectionTh, na.rm = na.rm, convertNuID = FALSE,  :
  formal argument "convertNuID" matched by multiple actual arguments

If I remove convertNuID=TRUE, it works fine but featureNames are defined by ProbeID.

After I read this I want to play with matrix generated by "exprs()" and rownames is always same with probeID.

There is an another argument in lumiR.idat, probeID. However, there is no changes when I select ProbeID or NuID.

I want the rownames are NuID or EntrezID at the end. And can you please let me know how I can do it?

Best regards,

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
(office) 212-659-6877




On Aug 27, 2012, at 8:40 PM, Mark Cowley wrote:

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@gmail.com<mailto:grimbough@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@mssm.edu<mailto:seungyeul.yoo@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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--
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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