Hi Mike,

Thank you so much for your advice. I can now install it properly and succeeded to read a idat file.

After I read a idat file, then it contains information something like following.

> idat[1:10,]
   MeanBinData TrimmedMeanBinData DevBinData MedianBinData BackgroundBinData BackgroundDevBinData CodesBinData NumBeadsBinData
1    577.37201          586.94641  102.94595     563.49585                 0                    0        10008              21
2    105.32843          107.54086   17.36357     102.84825                 0                    0        10010              18
3    105.47916          106.90141   23.27995      98.20106                 0                    0        10014              26
4     96.03654           97.22727   12.01887      93.85848                 0                    0        10017              18
5    101.15079          102.46756   14.26707     102.40277                 0                    0        10019              21
6    110.97807          111.94042   15.54425     108.54636                 0                    0        10020              25
7     93.36533           94.80687   12.88733      91.90852                 0                    0        10021              17
8    103.91557          105.35213   19.37169     102.13950                 0                    0        10025              22
9    105.39189          106.81569   12.94761     107.72005                 0                    0        10026              19
10   100.90147          102.46033   18.38206      93.95204                 0                    0        10035              16
   NumGoodBeadsBinData IllumicodeBinData
1                   20             10008
2                   18             10010
3                   26             10014
4                   17             10017
5                   20             10019
6                   23             10020
7                   16             10021
8                   21             10025
9                   19             10026
10                  16             10035

This is my first time to analyze gene expression of idat file, so please let me ask a few naive questions.

1) Is CodesBinData (which is identical with IllumicodeBinData here) same as probe ID?
2) What value would be compared with other samples as gene expression level? MeanBinData or TrimmedMeanBinData?
3) It this data processed or pre-processed (i.e background correction or normalization)?
4) Is there any other known package I can work on from this point to proceed analysis?

Thank you so much for your help.

Best regards,

Seungyeul


On Aug 25, 2012, at 3:12 PM, Mike Smith 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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